diff --git a/docs/cli-reference/index.md b/docs/cli-reference/index.md
index f7a3d7886..739d4dda3 100644
--- a/docs/cli-reference/index.md
+++ b/docs/cli-reference/index.md
@@ -112,6 +112,7 @@ This documentation is auto-generated from test cases.
 
 - [`--no-alias`](field-customization.md#no-alias)
 - [`--no-color`](utility-options.md#no-color)
+- [`--no-treat-dot-as-module`](template-customization.md#no-treat-dot-as-module)
 - [`--no-use-specialized-enum`](typing-customization.md#no-use-specialized-enum)
 - [`--no-use-standard-collections`](typing-customization.md#no-use-standard-collections)
 - [`--no-use-union-operator`](typing-customization.md#no-use-union-operator)
@@ -150,7 +151,6 @@ This documentation is auto-generated from test cases.
 ### T {#t}
 
 - [`--target-python-version`](model-customization.md#target-python-version)
-- [`--treat-dot-as-module`](template-customization.md#treat-dot-as-module)
 - [`--type-mappings`](typing-customization.md#type-mappings)
 
 ### U {#u}
diff --git a/docs/cli-reference/quick-reference.md b/docs/cli-reference/quick-reference.md
index c8b2b343c..ffca85484 100644
--- a/docs/cli-reference/quick-reference.md
+++ b/docs/cli-reference/quick-reference.md
@@ -119,7 +119,7 @@ datamodel-codegen [OPTIONS]
 | [`--enable-version-header`](template-customization.md#enable-version-header) | Include tool version information in file header. |
 | [`--extra-template-data`](template-customization.md#extra-template-data) | Pass custom template variables from JSON file for code generation. |
 | [`--formatters`](template-customization.md#formatters) | Specify code formatters to apply to generated output. |
-| [`--treat-dot-as-module`](template-customization.md#treat-dot-as-module) | Treat dots in schema names as module separators. |
+| [`--no-treat-dot-as-module`](template-customization.md#no-treat-dot-as-module) | Keep dots in schema names as underscores for flat output. |
 | [`--use-double-quotes`](template-customization.md#use-double-quotes) | Use double quotes for string literals in generated code. |
 | [`--use-exact-imports`](template-customization.md#use-exact-imports) | Import exact types instead of modules. |
 | [`--wrap-string-literal`](template-customization.md#wrap-string-literal) | Wrap long string literals across multiple lines. |
@@ -225,6 +225,7 @@ All options sorted alphabetically:
 - [`--module-split-mode`](general-options.md#module-split-mode) - Split generated models into separate files, one per model cl...
 - [`--no-alias`](field-customization.md#no-alias) - Disable Field alias generation for non-Python-safe property ...
 - [`--no-color`](utility-options.md#no-color) - Disable colorized output
+- [`--no-treat-dot-as-module`](template-customization.md#no-treat-dot-as-module) - Keep dots in schema names as underscores for flat output.
 - [`--no-use-specialized-enum`](typing-customization.md#no-use-specialized-enum) - Disable specialized Enum classes for Python 3.11+ code gener...
 - [`--no-use-standard-collections`](typing-customization.md#no-use-standard-collections) - Use built-in dict/list instead of typing.Dict/List.
 - [`--no-use-union-operator`](typing-customization.md#no-use-union-operator) - Test GraphQL annotated types with standard collections and u...
@@ -248,7 +249,6 @@ All options sorted alphabetically:
 - [`--strict-types`](typing-customization.md#strict-types) - Enable strict type validation for specified Python types.
 - [`--strip-default-none`](model-customization.md#strip-default-none) - Remove fields with None as default value from generated mode...
 - [`--target-python-version`](model-customization.md#target-python-version) - Target Python version for generated code syntax and imports.
-- [`--treat-dot-as-module`](template-customization.md#treat-dot-as-module) - Treat dots in schema names as module separators.
 - [`--type-mappings`](typing-customization.md#type-mappings) - Override default type mappings for schema formats.
 - [`--union-mode`](model-customization.md#union-mode) - Union mode for combining anyOf/oneOf schemas (smart or left_...
 - [`--url`](base-options.md#url) - Fetch schema from URL with custom HTTP headers.
diff --git a/docs/cli-reference/template-customization.md b/docs/cli-reference/template-customization.md
index ff23c27f1..2f7d37a22 100644
--- a/docs/cli-reference/template-customization.md
+++ b/docs/cli-reference/template-customization.md
@@ -16,7 +16,7 @@
 | [`--enable-version-header`](#enable-version-header) | Include tool version information in file header. |
 | [`--extra-template-data`](#extra-template-data) | Pass custom template variables from JSON file for code gener... |
 | [`--formatters`](#formatters) | Specify code formatters to apply to generated output. |
-| [`--treat-dot-as-module`](#treat-dot-as-module) | Treat dots in schema names as module separators. |
+| [`--no-treat-dot-as-module`](#no-treat-dot-as-module) | Keep dots in schema names as underscores for flat output. |
 | [`--use-double-quotes`](#use-double-quotes) | Use double quotes for string literals in generated code. |
 | [`--use-exact-imports`](#use-exact-imports) | Import exact types instead of modules. |
 | [`--wrap-string-literal`](#wrap-string-literal) | Wrap long string literals across multiple lines. |
@@ -2260,21 +2260,21 @@ Use this to customize formatting or disable formatters entirely.
 
 ---
 
-## `--treat-dot-as-module` {#treat-dot-as-module}
+## `--no-treat-dot-as-module` {#no-treat-dot-as-module}
 
-Treat dots in schema names as module separators.
+Keep dots in schema names as underscores for flat output.
 
-The `--treat-dot-as-module` flag configures the code generation behavior.
+The `--no-treat-dot-as-module` flag prevents splitting dotted schema names.
 
 **See also:** [Module Structure and Exports](../module-exports.md)
 
 !!! tip "Usage"
 
     ```bash
-    datamodel-codegen --input schema.json --treat-dot-as-module # (1)!
+    datamodel-codegen --input schema.json --no-treat-dot-as-module # (1)!
     ```
 
-    1. :material-arrow-left: `--treat-dot-as-module` - the option documented here
+    1. :material-arrow-left: `--no-treat-dot-as-module` - the option documented here
 
 ??? example "Examples"
 
@@ -2306,12 +2306,7 @@ The `--treat-dot-as-module` flag configures the code generation behavior.
     #   filename:  treat_dot_as_module_single
     #   timestamp: 2019-07-26T00:00:00+00:00
     
-    # model/__init__.py
-    # generated by datamodel-codegen:
-    #   filename:  treat_dot_as_module_single
-    #   timestamp: 2019-07-26T00:00:00+00:00
-    
-    # model/schema.py
+    # model_schema.py
     # generated by datamodel-codegen:
     #   filename:  model.schema.json
     #   timestamp: 2019-07-26T00:00:00+00:00
diff --git a/src/datamodel_code_generator/__init__.py b/src/datamodel_code_generator/__init__.py
index 3008dfb09..e7d5ce186 100644
--- a/src/datamodel_code_generator/__init__.py
+++ b/src/datamodel_code_generator/__init__.py
@@ -465,7 +465,7 @@ def generate(  # noqa: PLR0912, PLR0913, PLR0914, PLR0915
     custom_formatters_kwargs: dict[str, Any] | None = None,
     use_pendulum: bool = False,
     http_query_parameters: Sequence[tuple[str, str]] | None = None,
-    treat_dot_as_module: bool = False,
+    treat_dot_as_module: bool | None = None,
     use_exact_imports: bool = False,
     union_mode: UnionMode | None = None,
     output_datetime_class: DatetimeClassType | None = None,
diff --git a/src/datamodel_code_generator/__main__.py b/src/datamodel_code_generator/__main__.py
index fb2791d2e..03928ecb3 100644
--- a/src/datamodel_code_generator/__main__.py
+++ b/src/datamodel_code_generator/__main__.py
@@ -452,7 +452,7 @@ def validate_all_exports_collision_strategy(cls, values: dict[str, Any]) -> dict
     custom_formatters_kwargs: Optional[TextIOBase] = None  # noqa: UP045
     use_pendulum: bool = False
     http_query_parameters: Optional[Sequence[tuple[str, str]]] = None  # noqa: UP045
-    treat_dot_as_module: bool = False
+    treat_dot_as_module: Optional[bool] = None  # noqa: UP045
     use_exact_imports: bool = False
     union_mode: Optional[UnionMode] = None  # noqa: UP045
     output_datetime_class: Optional[DatetimeClassType] = None  # noqa: UP045
diff --git a/src/datamodel_code_generator/arguments.py b/src/datamodel_code_generator/arguments.py
index 9cedb2ef6..464ba5408 100644
--- a/src/datamodel_code_generator/arguments.py
+++ b/src/datamodel_code_generator/arguments.py
@@ -272,8 +272,9 @@ def start_section(self, heading: str | None) -> None:
 )
 model_options.add_argument(
     "--treat-dot-as-module",
-    help="treat dotted module names as modules",
-    action="store_true",
+    help="Treat dotted schema names as module paths, creating nested directory structures (e.g., 'foo.bar.Model' "
+    "becomes 'foo/bar.py'). Use --no-treat-dot-as-module to keep dots in names as underscores for single-file output.",
+    action=BooleanOptionalAction,
     default=None,
 )
 model_options.add_argument(
diff --git a/src/datamodel_code_generator/cli_options.py b/src/datamodel_code_generator/cli_options.py
index fc86244e8..9161747e4 100644
--- a/src/datamodel_code_generator/cli_options.py
+++ b/src/datamodel_code_generator/cli_options.py
@@ -177,7 +177,7 @@ class CLIOptionMeta:
     "--disable-appending-item-suffix": CLIOptionMeta(
         name="--disable-appending-item-suffix", category=OptionCategory.TEMPLATE
     ),
-    "--treat-dot-as-module": CLIOptionMeta(name="--treat-dot-as-module", category=OptionCategory.TEMPLATE),
+    "--no-treat-dot-as-module": CLIOptionMeta(name="--no-treat-dot-as-module", category=OptionCategory.TEMPLATE),
     "--disable-timestamp": CLIOptionMeta(name="--disable-timestamp", category=OptionCategory.TEMPLATE),
     "--enable-version-header": CLIOptionMeta(name="--enable-version-header", category=OptionCategory.TEMPLATE),
     "--enable-command-header": CLIOptionMeta(name="--enable-command-header", category=OptionCategory.TEMPLATE),
diff --git a/src/datamodel_code_generator/model/base.py b/src/datamodel_code_generator/model/base.py
index 47a7f7467..a44c57253 100644
--- a/src/datamodel_code_generator/model/base.py
+++ b/src/datamodel_code_generator/model/base.py
@@ -406,8 +406,12 @@ def get_template(template_file_path: Path) -> Template:
     return environment.get_template(template_file_path.name)
 
 
-def sanitize_module_name(name: str, *, treat_dot_as_module: bool) -> str:
-    """Sanitize a module name by replacing invalid characters."""
+def sanitize_module_name(name: str, *, treat_dot_as_module: bool | None) -> str:
+    """Sanitize a module name by replacing invalid characters.
+
+    If treat_dot_as_module is True, dots are preserved in the name.
+    If treat_dot_as_module is False or None (default), dots are replaced with underscores.
+    """
     pattern = r"[^0-9a-zA-Z_.]" if treat_dot_as_module else r"[^0-9a-zA-Z_]"
     sanitized = re.sub(pattern, "_", name)
     if sanitized and sanitized[0].isdigit():
@@ -415,19 +419,28 @@ def sanitize_module_name(name: str, *, treat_dot_as_module: bool) -> str:
     return sanitized
 
 
-def get_module_path(name: str, file_path: Path | None, *, treat_dot_as_module: bool) -> list[str]:
-    """Get the module path components from a name and file path."""
+def get_module_path(name: str, file_path: Path | None, *, treat_dot_as_module: bool | None) -> list[str]:
+    """Get the module path components from a name and file path.
+
+    The treat_dot_as_module flag controls behavior:
+    - None (default): Split names on dots (backward compat), but sanitize file names (replace dots)
+    - True: Split names on dots AND keep dots in file names (for modular output)
+    - False: Don't split names on dots AND sanitize file names (new feature for flat output)
+    """
+    should_split_names = treat_dot_as_module is not False
+    should_keep_dots_in_files = treat_dot_as_module is True
     if file_path:
-        sanitized_stem = sanitize_module_name(file_path.stem, treat_dot_as_module=treat_dot_as_module)
+        sanitized_stem = sanitize_module_name(file_path.stem, treat_dot_as_module=should_keep_dots_in_files)
+        module_parts = name.split(".")[:-1] if should_split_names else []
         return [
             *file_path.parts[:-1],
             sanitized_stem,
-            *name.split(".")[:-1],
+            *module_parts,
         ]
-    return name.split(".")[:-1]
+    return name.split(".")[:-1] if should_split_names else []
 
 
-def get_module_name(name: str, file_path: Path | None, *, treat_dot_as_module: bool) -> str:
+def get_module_name(name: str, file_path: Path | None, *, treat_dot_as_module: bool | None) -> str:
     """Get the full module name from a name and file path."""
     return ".".join(get_module_path(name, file_path, treat_dot_as_module=treat_dot_as_module))
 
@@ -501,7 +514,7 @@ def __init__(  # noqa: PLR0913
         nullable: bool = False,
         keyword_only: bool = False,
         frozen: bool = False,
-        treat_dot_as_module: bool = False,
+        treat_dot_as_module: bool | None = None,
         dataclass_arguments: DataclassArguments | None = None,
     ) -> None:
         """Initialize a data model with fields, base classes, and configuration."""
@@ -561,7 +574,7 @@ def __init__(  # noqa: PLR0913
         self._additional_imports.extend(self.DEFAULT_IMPORTS)
         self.default: Any = default
         self._nullable: bool = nullable
-        self._treat_dot_as_module: bool = treat_dot_as_module
+        self._treat_dot_as_module: bool | None = treat_dot_as_module
 
     def _validate_fields(self, fields: list[DataModelFieldBase]) -> list[DataModelFieldBase]:
         names: set[str] = set()
@@ -721,7 +734,7 @@ def create_base_class_model(
         reference: Reference,  # noqa: ARG003
         custom_template_dir: Path | None = None,  # noqa: ARG003
         keyword_only: bool = False,  # noqa: ARG003, FBT001, FBT002
-        treat_dot_as_module: bool = False,  # noqa: ARG003, FBT001, FBT002
+        treat_dot_as_module: bool | None = None,  # noqa: ARG003, FBT001
     ) -> DataModel | None:
         """Create a shared base class model for DRY configuration.
 
diff --git a/src/datamodel_code_generator/model/dataclass.py b/src/datamodel_code_generator/model/dataclass.py
index 545b6c42c..836313c2e 100644
--- a/src/datamodel_code_generator/model/dataclass.py
+++ b/src/datamodel_code_generator/model/dataclass.py
@@ -62,7 +62,7 @@ def __init__(  # noqa: PLR0913
         nullable: bool = False,
         keyword_only: bool = False,
         frozen: bool = False,
-        treat_dot_as_module: bool = False,
+        treat_dot_as_module: bool | None = None,
         dataclass_arguments: DataclassArguments | None = None,
     ) -> None:
         """Initialize dataclass with fields sorted by field assignment requirement."""
@@ -218,7 +218,7 @@ def __init__(  # noqa: PLR0913, PLR0917
         use_union_operator: bool = False,  # noqa: FBT001, FBT002
         use_pendulum: bool = False,  # noqa: FBT001, FBT002
         target_datetime_class: DatetimeClassType = DatetimeClassType.Datetime,
-        treat_dot_as_module: bool = False,  # noqa: FBT001, FBT002
+        treat_dot_as_module: bool | None = None,  # noqa: FBT001
         use_serialize_as_any: bool = False,  # noqa: FBT001, FBT002
     ) -> None:
         """Initialize type manager with datetime type mapping."""
diff --git a/src/datamodel_code_generator/model/enum.py b/src/datamodel_code_generator/model/enum.py
index fda352d12..403ab599b 100644
--- a/src/datamodel_code_generator/model/enum.py
+++ b/src/datamodel_code_generator/model/enum.py
@@ -61,7 +61,7 @@ def __init__(  # noqa: PLR0913
         default: Any = UNDEFINED,
         nullable: bool = False,
         keyword_only: bool = False,
-        treat_dot_as_module: bool = False,
+        treat_dot_as_module: bool | None = None,
     ) -> None:
         """Initialize Enum with optional specialized base class based on type."""
         super().__init__(
diff --git a/src/datamodel_code_generator/model/msgspec.py b/src/datamodel_code_generator/model/msgspec.py
index e6d9ac1ed..47f01a4ad 100644
--- a/src/datamodel_code_generator/model/msgspec.py
+++ b/src/datamodel_code_generator/model/msgspec.py
@@ -140,7 +140,7 @@ def __init__(  # noqa: PLR0913
         default: Any = UNDEFINED,
         nullable: bool = False,
         keyword_only: bool = False,
-        treat_dot_as_module: bool = False,
+        treat_dot_as_module: bool | None = None,
     ) -> None:
         """Initialize msgspec Struct with fields sorted by field assignment requirement."""
         super().__init__(
@@ -174,7 +174,7 @@ def create_base_class_model(
         reference: Reference,
         custom_template_dir: Path | None = None,
         keyword_only: bool = False,  # noqa: FBT001, FBT002
-        treat_dot_as_module: bool = False,  # noqa: FBT001, FBT002
+        treat_dot_as_module: bool | None = None,  # noqa: FBT001
     ) -> Struct | None:
         """Create a shared base class model for DRY configuration.
 
@@ -504,7 +504,7 @@ def __init__(  # noqa: PLR0913, PLR0917
         use_union_operator: bool = False,  # noqa: FBT001, FBT002
         use_pendulum: bool = False,  # noqa: FBT001, FBT002
         target_datetime_class: DatetimeClassType | None = None,
-        treat_dot_as_module: bool = False,  # noqa: FBT001, FBT002
+        treat_dot_as_module: bool | None = None,  # noqa: FBT001
         use_serialize_as_any: bool = False,  # noqa: FBT001, FBT002
     ) -> None:
         """Initialize type manager with optional datetime type mapping."""
diff --git a/src/datamodel_code_generator/model/pydantic/base_model.py b/src/datamodel_code_generator/model/pydantic/base_model.py
index 57d88711c..b81b5ecbe 100644
--- a/src/datamodel_code_generator/model/pydantic/base_model.py
+++ b/src/datamodel_code_generator/model/pydantic/base_model.py
@@ -288,7 +288,7 @@ def __init__(  # noqa: PLR0913
         default: Any = UNDEFINED,
         nullable: bool = False,
         keyword_only: bool = False,
-        treat_dot_as_module: bool = False,
+        treat_dot_as_module: bool | None = None,
     ) -> None:
         """Initialize the BaseModel with fields and configuration."""
         methods: list[str] = [field.method for field in fields if field.method]
@@ -345,7 +345,7 @@ def __init__(  # noqa: PLR0912, PLR0913
         default: Any = UNDEFINED,
         nullable: bool = False,
         keyword_only: bool = False,
-        treat_dot_as_module: bool = False,
+        treat_dot_as_module: bool | None = None,
     ) -> None:
         """Initialize the BaseModel with Config and extra fields support."""
         super().__init__(
diff --git a/src/datamodel_code_generator/model/pydantic/types.py b/src/datamodel_code_generator/model/pydantic/types.py
index 69c021ec8..c2c1edb02 100644
--- a/src/datamodel_code_generator/model/pydantic/types.py
+++ b/src/datamodel_code_generator/model/pydantic/types.py
@@ -181,7 +181,7 @@ def __init__(  # noqa: PLR0913, PLR0917
         use_union_operator: bool = False,  # noqa: FBT001, FBT002
         use_pendulum: bool = False,  # noqa: FBT001, FBT002
         target_datetime_class: DatetimeClassType | None = None,
-        treat_dot_as_module: bool = False,  # noqa: FBT001, FBT002
+        treat_dot_as_module: bool | None = None,  # noqa: FBT001
         use_serialize_as_any: bool = False,  # noqa: FBT001, FBT002
     ) -> None:
         """Initialize the DataTypeManager with Pydantic v1 type mappings."""
diff --git a/src/datamodel_code_generator/model/pydantic_v2/base_model.py b/src/datamodel_code_generator/model/pydantic_v2/base_model.py
index 97e8d0db7..f2d267e06 100644
--- a/src/datamodel_code_generator/model/pydantic_v2/base_model.py
+++ b/src/datamodel_code_generator/model/pydantic_v2/base_model.py
@@ -200,7 +200,7 @@ def __init__(  # noqa: PLR0913
         default: Any = UNDEFINED,
         nullable: bool = False,
         keyword_only: bool = False,
-        treat_dot_as_module: bool = False,
+        treat_dot_as_module: bool | None = None,
     ) -> None:
         """Initialize BaseModel with ConfigDict generation from template data."""
         super().__init__(
@@ -285,7 +285,7 @@ def create_base_class_model(
         reference: Reference,
         custom_template_dir: Path | None = None,
         keyword_only: bool = False,  # noqa: FBT001, FBT002
-        treat_dot_as_module: bool = False,  # noqa: FBT001, FBT002
+        treat_dot_as_module: bool | None = None,  # noqa: FBT001
     ) -> BaseModel | None:
         """Create a shared base class model for DRY configuration.
 
diff --git a/src/datamodel_code_generator/model/pydantic_v2/types.py b/src/datamodel_code_generator/model/pydantic_v2/types.py
index 7a3bba049..3b0a7a6e0 100644
--- a/src/datamodel_code_generator/model/pydantic_v2/types.py
+++ b/src/datamodel_code_generator/model/pydantic_v2/types.py
@@ -80,7 +80,7 @@ def __init__(  # noqa: PLR0913, PLR0917
         use_union_operator: bool = False,  # noqa: FBT001, FBT002
         use_pendulum: bool = False,  # noqa: FBT001, FBT002
         target_datetime_class: DatetimeClassType | None = None,
-        treat_dot_as_module: bool = False,  # noqa: FBT001, FBT002
+        treat_dot_as_module: bool | None = None,  # noqa: FBT001
         use_serialize_as_any: bool = False,  # noqa: FBT001, FBT002
     ) -> None:
         """Initialize with pydantic v2-specific DataType."""
diff --git a/src/datamodel_code_generator/model/scalar.py b/src/datamodel_code_generator/model/scalar.py
index 9fa9e58c8..927088fc7 100644
--- a/src/datamodel_code_generator/model/scalar.py
+++ b/src/datamodel_code_generator/model/scalar.py
@@ -57,7 +57,7 @@ def __init__(  # noqa: PLR0913
         default: Any = UNDEFINED,
         nullable: bool = False,
         keyword_only: bool = False,
-        treat_dot_as_module: bool = False,
+        treat_dot_as_module: bool | None = None,
     ) -> None:
         """Initialize GraphQL scalar type with Python type mapping."""
         extra_template_data = extra_template_data or defaultdict(dict)
diff --git a/src/datamodel_code_generator/model/typed_dict.py b/src/datamodel_code_generator/model/typed_dict.py
index 73ac45a70..7ec425af4 100644
--- a/src/datamodel_code_generator/model/typed_dict.py
+++ b/src/datamodel_code_generator/model/typed_dict.py
@@ -67,7 +67,7 @@ def __init__(  # noqa: PLR0913
         default: Any = UNDEFINED,
         nullable: bool = False,
         keyword_only: bool = False,
-        treat_dot_as_module: bool = False,
+        treat_dot_as_module: bool | None = None,
     ) -> None:
         """Initialize TypedDict model."""
         super().__init__(
diff --git a/src/datamodel_code_generator/model/types.py b/src/datamodel_code_generator/model/types.py
index 05aad2ca4..ed4a41053 100644
--- a/src/datamodel_code_generator/model/types.py
+++ b/src/datamodel_code_generator/model/types.py
@@ -84,7 +84,7 @@ def __init__(  # noqa: PLR0913, PLR0917
         use_union_operator: bool = False,  # noqa: FBT001, FBT002
         use_pendulum: bool = False,  # noqa: FBT001, FBT002
         target_datetime_class: DatetimeClassType | None = None,
-        treat_dot_as_module: bool = False,  # noqa: FBT001, FBT002
+        treat_dot_as_module: bool | None = None,  # noqa: FBT001
         use_serialize_as_any: bool = False,  # noqa: FBT001, FBT002
     ) -> None:
         """Initialize type manager with basic type mapping."""
diff --git a/src/datamodel_code_generator/model/union.py b/src/datamodel_code_generator/model/union.py
index c0a119ae5..e24d94144 100644
--- a/src/datamodel_code_generator/model/union.py
+++ b/src/datamodel_code_generator/model/union.py
@@ -42,7 +42,7 @@ def __init__(  # noqa: PLR0913
         default: Any = UNDEFINED,
         nullable: bool = False,
         keyword_only: bool = False,
-        treat_dot_as_module: bool = False,
+        treat_dot_as_module: bool | None = None,
     ) -> None:
         """Initialize GraphQL union type."""
         super().__init__(
diff --git a/src/datamodel_code_generator/parser/base.py b/src/datamodel_code_generator/parser/base.py
index 253a2ea51..169065c58 100644
--- a/src/datamodel_code_generator/parser/base.py
+++ b/src/datamodel_code_generator/parser/base.py
@@ -756,7 +756,7 @@ def __init__(  # noqa: PLR0912, PLR0913, PLR0915
         custom_formatters_kwargs: dict[str, Any] | None = None,
         use_pendulum: bool = False,
         http_query_parameters: Sequence[tuple[str, str]] | None = None,
-        treat_dot_as_module: bool = False,
+        treat_dot_as_module: bool | None = None,
         use_exact_imports: bool = False,
         default_field_extras: dict[str, Any] | None = None,
         target_datetime_class: DatetimeClassType | None = None,
@@ -784,7 +784,7 @@ def __init__(  # noqa: PLR0912, PLR0913, PLR0915
             use_union_operator=use_union_operator,
             use_pendulum=use_pendulum,
             target_datetime_class=target_datetime_class,
-            treat_dot_as_module=treat_dot_as_module,
+            treat_dot_as_module=treat_dot_as_module or False,
             use_serialize_as_any=use_serialize_as_any,
         )
         self.data_model_type: type[DataModel] = data_model_type
diff --git a/src/datamodel_code_generator/parser/graphql.py b/src/datamodel_code_generator/parser/graphql.py
index 3ee1974d7..5e7ba4161 100644
--- a/src/datamodel_code_generator/parser/graphql.py
+++ b/src/datamodel_code_generator/parser/graphql.py
@@ -178,7 +178,7 @@ def __init__(  # noqa: PLR0913
         custom_formatters_kwargs: dict[str, Any] | None = None,
         use_pendulum: bool = False,
         http_query_parameters: Sequence[tuple[str, str]] | None = None,
-        treat_dot_as_module: bool = False,
+        treat_dot_as_module: bool | None = None,
         use_exact_imports: bool = False,
         default_field_extras: dict[str, Any] | None = None,
         target_datetime_class: DatetimeClassType = DatetimeClassType.Datetime,
diff --git a/src/datamodel_code_generator/parser/jsonschema.py b/src/datamodel_code_generator/parser/jsonschema.py
index 8e69d3a50..601841537 100644
--- a/src/datamodel_code_generator/parser/jsonschema.py
+++ b/src/datamodel_code_generator/parser/jsonschema.py
@@ -591,7 +591,7 @@ def __init__(  # noqa: PLR0913
         custom_formatters_kwargs: dict[str, Any] | None = None,
         use_pendulum: bool = False,
         http_query_parameters: Sequence[tuple[str, str]] | None = None,
-        treat_dot_as_module: bool = False,
+        treat_dot_as_module: bool | None = None,
         use_exact_imports: bool = False,
         default_field_extras: dict[str, Any] | None = None,
         target_datetime_class: DatetimeClassType | None = None,
diff --git a/src/datamodel_code_generator/parser/openapi.py b/src/datamodel_code_generator/parser/openapi.py
index 9d9511421..c7dc601a5 100644
--- a/src/datamodel_code_generator/parser/openapi.py
+++ b/src/datamodel_code_generator/parser/openapi.py
@@ -262,7 +262,7 @@ def __init__(  # noqa: PLR0913
         custom_formatters_kwargs: dict[str, Any] | None = None,
         use_pendulum: bool = False,
         http_query_parameters: Sequence[tuple[str, str]] | None = None,
-        treat_dot_as_module: bool = False,
+        treat_dot_as_module: bool | None = None,
         use_exact_imports: bool = False,
         default_field_extras: dict[str, Any] | None = None,
         target_datetime_class: DatetimeClassType | None = None,
diff --git a/src/datamodel_code_generator/reference.py b/src/datamodel_code_generator/reference.py
index e6b944a9c..a420284b8 100644
--- a/src/datamodel_code_generator/reference.py
+++ b/src/datamodel_code_generator/reference.py
@@ -515,7 +515,7 @@ def __init__(  # noqa: PLR0913, PLR0917
         no_alias: bool = False,  # noqa: FBT001, FBT002
         remove_suffix_number: bool = False,  # noqa: FBT001, FBT002
         parent_scoped_naming: bool = False,  # noqa: FBT001, FBT002
-        treat_dot_as_module: bool = False,  # noqa: FBT001, FBT002
+        treat_dot_as_module: bool | None = None,  # noqa: FBT001
     ) -> None:
         """Initialize model resolver with naming and resolution options."""
         self.references: dict[str, Reference] = {}
@@ -854,7 +854,7 @@ def get_class_name(
         singular_name_suffix: str | None = None,
     ) -> ClassName:
         """Generate a unique class name with optional singularization."""
-        if "." in name:
+        if "." in name and self.treat_dot_as_module is not False:
             split_name = name.split(".")
             prefix = ".".join(
                 # TODO: create a validate for class name
@@ -865,7 +865,7 @@ def get_class_name(
             class_name = split_name[-1]
         else:
             prefix = ""
-            class_name = name
+            class_name = name.replace(".", "_") if "." in name else name
 
         class_name = self.class_name_generator(class_name)
 
diff --git a/src/datamodel_code_generator/types.py b/src/datamodel_code_generator/types.py
index eca9192b7..e1a6340f4 100644
--- a/src/datamodel_code_generator/types.py
+++ b/src/datamodel_code_generator/types.py
@@ -825,7 +825,7 @@ def __init__(  # noqa: PLR0913, PLR0917
         use_union_operator: bool = False,  # noqa: FBT001, FBT002
         use_pendulum: bool = False,  # noqa: FBT001, FBT002
         target_datetime_class: DatetimeClassType | None = None,
-        treat_dot_as_module: bool = False,  # noqa: FBT001, FBT002
+        treat_dot_as_module: bool | None = None,  # noqa: FBT001
         use_serialize_as_any: bool = False,  # noqa: FBT001, FBT002
     ) -> None:
         """Initialize DataTypeManager with code generation options."""
@@ -840,7 +840,7 @@ def __init__(  # noqa: PLR0913, PLR0917
         self.use_union_operator: bool = use_union_operator
         self.use_pendulum: bool = use_pendulum
         self.target_datetime_class: DatetimeClassType | None = target_datetime_class
-        self.treat_dot_as_module: bool = treat_dot_as_module
+        self.treat_dot_as_module: bool = treat_dot_as_module or False
         self.use_serialize_as_any: bool = use_serialize_as_any
 
         self.data_type: type[DataType] = create_model(
diff --git a/tests/data/expected/main/jsonschema/no_treat_dot_single/__init__.py b/tests/data/expected/main/jsonschema/no_treat_dot_single/__init__.py
new file mode 100644
index 000000000..dd8f594f7
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/no_treat_dot_single/__init__.py
@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  no_treat_dot_single
+#   timestamp: 2019-07-26T00:00:00+00:00
diff --git a/tests/data/expected/main/jsonschema/no_treat_dot_single/v0_0_39_job.py b/tests/data/expected/main/jsonschema/no_treat_dot_single/v0_0_39_job.py
new file mode 100644
index 000000000..72a040866
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/no_treat_dot_single/v0_0_39_job.py
@@ -0,0 +1,12 @@
+# generated by datamodel-codegen:
+#   filename:  v0.0.39.job.json
+#   timestamp: 2019-07-26T00:00:00+00:00
+
+from __future__ import annotations
+
+from pydantic import BaseModel
+
+
+class Job(BaseModel):
+    id: int
+    name: str
diff --git a/tests/data/expected/main/jsonschema/treat_dot_as_module_single_no_treat/__init__.py b/tests/data/expected/main/jsonschema/treat_dot_as_module_single_no_treat/__init__.py
new file mode 100644
index 000000000..ec0858be4
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_as_module_single_no_treat/__init__.py
@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  treat_dot_as_module_single
+#   timestamp: 2019-07-26T00:00:00+00:00
diff --git a/tests/data/expected/main/jsonschema/treat_dot_as_module_single_no_treat/model_schema.py b/tests/data/expected/main/jsonschema/treat_dot_as_module_single_no_treat/model_schema.py
new file mode 100644
index 000000000..6f026d6b2
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_as_module_single_no_treat/model_schema.py
@@ -0,0 +1,12 @@
+# generated by datamodel-codegen:
+#   filename:  model.schema.json
+#   timestamp: 2019-07-26T00:00:00+00:00
+
+from __future__ import annotations
+
+from pydantic import BaseModel
+
+
+class User(BaseModel):
+    name: str
+    age: int | None = None
diff --git a/tests/data/expected/main/jsonschema/treat_dot_complex_no_treat/__init__.py b/tests/data/expected/main/jsonschema/treat_dot_complex_no_treat/__init__.py
new file mode 100644
index 000000000..c982e8d9a
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_complex_no_treat/__init__.py
@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  treat_dot_complex
+#   timestamp: 2019-07-26T00:00:00+00:00
diff --git a/tests/data/expected/main/jsonschema/treat_dot_complex_no_treat/api_v1_address.py b/tests/data/expected/main/jsonschema/treat_dot_complex_no_treat/api_v1_address.py
new file mode 100644
index 000000000..85c0a534b
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_complex_no_treat/api_v1_address.py
@@ -0,0 +1,15 @@
+# generated by datamodel-codegen:
+#   filename:  api.v1.address.json
+#   timestamp: 2019-07-26T00:00:00+00:00
+
+from __future__ import annotations
+
+from pydantic import BaseModel
+
+from . import common_types_country
+
+
+class Address(BaseModel):
+    street: str | None = None
+    city: str | None = None
+    country: common_types_country.Country | None = None
diff --git a/tests/data/expected/main/jsonschema/treat_dot_complex_no_treat/api_v1_user.py b/tests/data/expected/main/jsonschema/treat_dot_complex_no_treat/api_v1_user.py
new file mode 100644
index 000000000..45b5cb0cf
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_complex_no_treat/api_v1_user.py
@@ -0,0 +1,16 @@
+# generated by datamodel-codegen:
+#   filename:  api.v1.user.json
+#   timestamp: 2019-07-26T00:00:00+00:00
+
+from __future__ import annotations
+
+from pydantic import BaseModel
+
+from . import api_v1_address, common_types_status
+
+
+class User(BaseModel):
+    id: int
+    name: str
+    address: api_v1_address.Address | None = None
+    status: common_types_status.Status | None = None
diff --git a/tests/data/expected/main/jsonschema/treat_dot_complex_no_treat/common_types_country.py b/tests/data/expected/main/jsonschema/treat_dot_complex_no_treat/common_types_country.py
new file mode 100644
index 000000000..d9f50b5e5
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_complex_no_treat/common_types_country.py
@@ -0,0 +1,12 @@
+# generated by datamodel-codegen:
+#   filename:  common.types.country.json
+#   timestamp: 2019-07-26T00:00:00+00:00
+
+from __future__ import annotations
+
+from pydantic import BaseModel, constr
+
+
+class Country(BaseModel):
+    code: constr(min_length=2, max_length=2)
+    name: str
diff --git a/tests/data/expected/main/jsonschema/treat_dot_complex_no_treat/common_types_status.py b/tests/data/expected/main/jsonschema/treat_dot_complex_no_treat/common_types_status.py
new file mode 100644
index 000000000..b7f2e792c
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_complex_no_treat/common_types_status.py
@@ -0,0 +1,13 @@
+# generated by datamodel-codegen:
+#   filename:  common.types.status.json
+#   timestamp: 2019-07-26T00:00:00+00:00
+
+from __future__ import annotations
+
+from enum import Enum
+
+
+class Status(Enum):
+    active = 'active'
+    inactive = 'inactive'
+    pending = 'pending'
diff --git a/tests/data/expected/main/jsonschema/treat_dot_complex_treat/__init__.py b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/__init__.py
new file mode 100644
index 000000000..c982e8d9a
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/__init__.py
@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  treat_dot_complex
+#   timestamp: 2019-07-26T00:00:00+00:00
diff --git a/tests/data/expected/main/jsonschema/treat_dot_complex_treat/api/__init__.py b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/api/__init__.py
new file mode 100644
index 000000000..c982e8d9a
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/api/__init__.py
@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  treat_dot_complex
+#   timestamp: 2019-07-26T00:00:00+00:00
diff --git a/tests/data/expected/main/jsonschema/treat_dot_complex_treat/api/v1/__init__.py b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/api/v1/__init__.py
new file mode 100644
index 000000000..c982e8d9a
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/api/v1/__init__.py
@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  treat_dot_complex
+#   timestamp: 2019-07-26T00:00:00+00:00
diff --git a/tests/data/expected/main/jsonschema/treat_dot_complex_treat/api/v1/address.py b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/api/v1/address.py
new file mode 100644
index 000000000..1ed253941
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/api/v1/address.py
@@ -0,0 +1,15 @@
+# generated by datamodel-codegen:
+#   filename:  api.v1.address.json
+#   timestamp: 2019-07-26T00:00:00+00:00
+
+from __future__ import annotations
+
+from pydantic import BaseModel
+
+from ...common.types import country as country_1
+
+
+class Address(BaseModel):
+    street: str | None = None
+    city: str | None = None
+    country: country_1.Country | None = None
diff --git a/tests/data/expected/main/jsonschema/treat_dot_complex_treat/api/v1/user.py b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/api/v1/user.py
new file mode 100644
index 000000000..06bccf5ba
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/api/v1/user.py
@@ -0,0 +1,17 @@
+# generated by datamodel-codegen:
+#   filename:  api.v1.user.json
+#   timestamp: 2019-07-26T00:00:00+00:00
+
+from __future__ import annotations
+
+from pydantic import BaseModel
+
+from ...common.types import status as status_1
+from . import address as address_1
+
+
+class User(BaseModel):
+    id: int
+    name: str
+    address: address_1.Address | None = None
+    status: status_1.Status | None = None
diff --git a/tests/data/expected/main/jsonschema/treat_dot_complex_treat/common/__init__.py b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/common/__init__.py
new file mode 100644
index 000000000..c982e8d9a
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/common/__init__.py
@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  treat_dot_complex
+#   timestamp: 2019-07-26T00:00:00+00:00
diff --git a/tests/data/expected/main/jsonschema/treat_dot_complex_treat/common/types/__init__.py b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/common/types/__init__.py
new file mode 100644
index 000000000..c982e8d9a
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/common/types/__init__.py
@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  treat_dot_complex
+#   timestamp: 2019-07-26T00:00:00+00:00
diff --git a/tests/data/expected/main/jsonschema/treat_dot_complex_treat/common/types/country.py b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/common/types/country.py
new file mode 100644
index 000000000..d9f50b5e5
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/common/types/country.py
@@ -0,0 +1,12 @@
+# generated by datamodel-codegen:
+#   filename:  common.types.country.json
+#   timestamp: 2019-07-26T00:00:00+00:00
+
+from __future__ import annotations
+
+from pydantic import BaseModel, constr
+
+
+class Country(BaseModel):
+    code: constr(min_length=2, max_length=2)
+    name: str
diff --git a/tests/data/expected/main/jsonschema/treat_dot_complex_treat/common/types/status.py b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/common/types/status.py
new file mode 100644
index 000000000..b7f2e792c
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_complex_treat/common/types/status.py
@@ -0,0 +1,13 @@
+# generated by datamodel-codegen:
+#   filename:  common.types.status.json
+#   timestamp: 2019-07-26T00:00:00+00:00
+
+from __future__ import annotations
+
+from enum import Enum
+
+
+class Status(Enum):
+    active = 'active'
+    inactive = 'inactive'
+    pending = 'pending'
diff --git a/tests/data/expected/main/jsonschema/treat_dot_single/__init__.py b/tests/data/expected/main/jsonschema/treat_dot_single/__init__.py
new file mode 100644
index 000000000..dd8f594f7
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_single/__init__.py
@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  no_treat_dot_single
+#   timestamp: 2019-07-26T00:00:00+00:00
diff --git a/tests/data/expected/main/jsonschema/treat_dot_single/v0/0/39/__init__.py b/tests/data/expected/main/jsonschema/treat_dot_single/v0/0/39/__init__.py
new file mode 100644
index 000000000..dd8f594f7
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_single/v0/0/39/__init__.py
@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  no_treat_dot_single
+#   timestamp: 2019-07-26T00:00:00+00:00
diff --git a/tests/data/expected/main/jsonschema/treat_dot_single/v0/0/39/job.py b/tests/data/expected/main/jsonschema/treat_dot_single/v0/0/39/job.py
new file mode 100644
index 000000000..72a040866
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_single/v0/0/39/job.py
@@ -0,0 +1,12 @@
+# generated by datamodel-codegen:
+#   filename:  v0.0.39.job.json
+#   timestamp: 2019-07-26T00:00:00+00:00
+
+from __future__ import annotations
+
+from pydantic import BaseModel
+
+
+class Job(BaseModel):
+    id: int
+    name: str
diff --git a/tests/data/expected/main/jsonschema/treat_dot_single/v0/0/__init__.py b/tests/data/expected/main/jsonschema/treat_dot_single/v0/0/__init__.py
new file mode 100644
index 000000000..dd8f594f7
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_single/v0/0/__init__.py
@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  no_treat_dot_single
+#   timestamp: 2019-07-26T00:00:00+00:00
diff --git a/tests/data/expected/main/jsonschema/treat_dot_single/v0/__init__.py b/tests/data/expected/main/jsonschema/treat_dot_single/v0/__init__.py
new file mode 100644
index 000000000..dd8f594f7
--- /dev/null
+++ b/tests/data/expected/main/jsonschema/treat_dot_single/v0/__init__.py
@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  no_treat_dot_single
+#   timestamp: 2019-07-26T00:00:00+00:00
diff --git a/tests/data/jsonschema/no_treat_dot_single/v0.0.39.job.json b/tests/data/jsonschema/no_treat_dot_single/v0.0.39.job.json
new file mode 100644
index 000000000..82f4591b0
--- /dev/null
+++ b/tests/data/jsonschema/no_treat_dot_single/v0.0.39.job.json
@@ -0,0 +1,14 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "title": "Job",
+  "type": "object",
+  "properties": {
+    "id": {
+      "type": "integer"
+    },
+    "name": {
+      "type": "string"
+    }
+  },
+  "required": ["id", "name"]
+}
diff --git a/tests/data/jsonschema/treat_dot_complex/api.v1.address.json b/tests/data/jsonschema/treat_dot_complex/api.v1.address.json
new file mode 100644
index 000000000..1fcca8138
--- /dev/null
+++ b/tests/data/jsonschema/treat_dot_complex/api.v1.address.json
@@ -0,0 +1,16 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "title": "Address",
+  "type": "object",
+  "properties": {
+    "street": {
+      "type": "string"
+    },
+    "city": {
+      "type": "string"
+    },
+    "country": {
+      "$ref": "common.types.country.json"
+    }
+  }
+}
diff --git a/tests/data/jsonschema/treat_dot_complex/api.v1.user.json b/tests/data/jsonschema/treat_dot_complex/api.v1.user.json
new file mode 100644
index 000000000..48fd4d406
--- /dev/null
+++ b/tests/data/jsonschema/treat_dot_complex/api.v1.user.json
@@ -0,0 +1,20 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "title": "User",
+  "type": "object",
+  "properties": {
+    "id": {
+      "type": "integer"
+    },
+    "name": {
+      "type": "string"
+    },
+    "address": {
+      "$ref": "api.v1.address.json"
+    },
+    "status": {
+      "$ref": "common.types.status.json"
+    }
+  },
+  "required": ["id", "name"]
+}
diff --git a/tests/data/jsonschema/treat_dot_complex/common.types.country.json b/tests/data/jsonschema/treat_dot_complex/common.types.country.json
new file mode 100644
index 000000000..1f882a45d
--- /dev/null
+++ b/tests/data/jsonschema/treat_dot_complex/common.types.country.json
@@ -0,0 +1,16 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "title": "Country",
+  "type": "object",
+  "properties": {
+    "code": {
+      "type": "string",
+      "minLength": 2,
+      "maxLength": 2
+    },
+    "name": {
+      "type": "string"
+    }
+  },
+  "required": ["code", "name"]
+}
diff --git a/tests/data/jsonschema/treat_dot_complex/common.types.status.json b/tests/data/jsonschema/treat_dot_complex/common.types.status.json
new file mode 100644
index 000000000..3760ff027
--- /dev/null
+++ b/tests/data/jsonschema/treat_dot_complex/common.types.status.json
@@ -0,0 +1,6 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "title": "Status",
+  "type": "string",
+  "enum": ["active", "inactive", "pending"]
+}
diff --git a/tests/main/jsonschema/test_main_jsonschema.py b/tests/main/jsonschema/test_main_jsonschema.py
index 1475e83a3..e183fd4cc 100644
--- a/tests/main/jsonschema/test_main_jsonschema.py
+++ b/tests/main/jsonschema/test_main_jsonschema.py
@@ -2353,15 +2353,20 @@ def test_main_use_union_operator(output_dir: Path) -> None:
     )
 
 
-@pytest.mark.parametrize("as_module", [True, False])
-def test_treat_dot_as_module(as_module: bool, output_dir: Path) -> None:
+@pytest.mark.parametrize(
+    ("extra_args", "expected_suffix"),
+    [
+        (["--treat-dot-as-module"], "treat_dot_as_module"),
+        (None, "treat_dot_not_as_module"),
+        (["--no-treat-dot-as-module"], "treat_dot_not_as_module"),
+    ],
+)
+def test_treat_dot_as_module(extra_args: list[str] | None, expected_suffix: str, output_dir: Path) -> None:
     """Test dot notation as module separator."""
-    path_extension = "treat_dot_as_module" if as_module else "treat_dot_not_as_module"
-    extra_args = ["--treat-dot-as-module"] if as_module else None
     run_main_and_assert(
         input_path=JSON_SCHEMA_DATA_PATH / "treat_dot_as_module",
         output_path=output_dir,
-        expected_directory=EXPECTED_JSON_SCHEMA_PATH / path_extension,
+        expected_directory=EXPECTED_JSON_SCHEMA_PATH / expected_suffix,
         extra_args=extra_args,
     )
 
@@ -2385,6 +2390,64 @@ def test_treat_dot_as_module_single_file(output_dir: Path) -> None:
     )
 
 
+@pytest.mark.cli_doc(
+    options=["--no-treat-dot-as-module"],
+    input_schema="jsonschema/treat_dot_as_module_single",
+    cli_args=["--no-treat-dot-as-module"],
+    golden_output="jsonschema/treat_dot_as_module_single_no_treat/",
+    primary=True,
+)
+def test_no_treat_dot_as_module_single_file(output_dir: Path) -> None:
+    """Keep dots in schema names as underscores for flat output.
+
+    The `--no-treat-dot-as-module` flag prevents splitting dotted schema names.
+    """
+    run_main_and_assert(
+        input_path=JSON_SCHEMA_DATA_PATH / "treat_dot_as_module_single",
+        output_path=output_dir,
+        expected_directory=EXPECTED_JSON_SCHEMA_PATH / "treat_dot_as_module_single_no_treat",
+        extra_args=["--no-treat-dot-as-module"],
+    )
+
+
+@pytest.mark.parametrize(
+    ("extra_args", "expected_suffix"),
+    [
+        (["--treat-dot-as-module"], "treat_dot_single"),
+        (None, "no_treat_dot_single"),
+        (["--no-treat-dot-as-module"], "no_treat_dot_single"),
+    ],
+)
+def test_treat_dot_as_module_version_style(
+    extra_args: list[str] | None, expected_suffix: str, output_dir: Path
+) -> None:
+    """Test dotted version-style schema names (e.g., v0.0.39.job.json)."""
+    run_main_and_assert(
+        input_path=JSON_SCHEMA_DATA_PATH / "no_treat_dot_single",
+        output_path=output_dir,
+        expected_directory=EXPECTED_JSON_SCHEMA_PATH / expected_suffix,
+        extra_args=extra_args,
+    )
+
+
+@pytest.mark.parametrize(
+    ("extra_args", "expected_suffix"),
+    [
+        (["--treat-dot-as-module"], "treat_dot_complex_treat"),
+        (None, "treat_dot_complex_no_treat"),
+        (["--no-treat-dot-as-module"], "treat_dot_complex_no_treat"),
+    ],
+)
+def test_treat_dot_as_module_complex_refs(extra_args: list[str] | None, expected_suffix: str, output_dir: Path) -> None:
+    """Test dotted schema names with cross-file references."""
+    run_main_and_assert(
+        input_path=JSON_SCHEMA_DATA_PATH / "treat_dot_complex",
+        output_path=output_dir,
+        expected_directory=EXPECTED_JSON_SCHEMA_PATH / expected_suffix,
+        extra_args=extra_args,
+    )
+
+
 def test_main_jsonschema_duplicate_name(output_dir: Path) -> None:
     """Test duplicate name handling."""
     run_main_and_assert(
diff --git a/tests/model/test_base.py b/tests/model/test_base.py
index f6e0fa4c2..29e09fa89 100644
--- a/tests/model/test_base.py
+++ b/tests/model/test_base.py
@@ -303,7 +303,7 @@ def test_sanitize_module_name(name: str, expected_true: str, expected_false: str
     ("treat_dot_as_module", "expected"),
     [
         (True, ["inputs", "array_commons.schema", "array-commons"]),
-        (False, ["inputs", "array_commons_schema", "array-commons"]),
+        (False, ["inputs", "array_commons_schema"]),
     ],
 )
 def test_get_module_path_with_file_path(treat_dot_as_module: bool, expected: list[str]) -> None:
@@ -313,23 +313,29 @@ def test_get_module_path_with_file_path(treat_dot_as_module: bool, expected: lis
     assert result == expected
 
 
-@pytest.mark.parametrize("treat_dot_as_module", [True, False])
-def test_get_module_path_without_file_path(treat_dot_as_module: bool) -> None:
-    """Test module path generation without a file path."""
-    result = get_module_path("my_module.submodule", None, treat_dot_as_module=treat_dot_as_module)
+def test_get_module_path_without_file_path_treat_dot_true() -> None:
+    """Test module path generation without a file path with treat_dot_as_module=True."""
+    result = get_module_path("my_module.submodule", None, treat_dot_as_module=True)
     expected = ["my_module"]
     assert result == expected
 
 
+def test_get_module_path_without_file_path_treat_dot_false() -> None:
+    """Test module path generation without a file path with treat_dot_as_module=False."""
+    result = get_module_path("my_module.submodule", None, treat_dot_as_module=False)
+    expected: list[str] = []
+    assert result == expected
+
+
 @pytest.mark.parametrize(
     ("treat_dot_as_module", "name", "expected"),
     [
         (True, "a.b.c", ["a", "b"]),
         (True, "simple", []),
         (True, "with.dot", ["with"]),
-        (False, "a.b.c", ["a", "b"]),
+        (False, "a.b.c", []),
         (False, "simple", []),
-        (False, "with.dot", ["with"]),
+        (False, "with.dot", []),
     ],
 )
 def test_get_module_path_without_file_path_parametrized(