diff --git a/tensorrt_llm/_torch/auto_deploy/models/hf.py b/tensorrt_llm/_torch/auto_deploy/models/hf.py
index f20c52babf..bf5384af15 100644
--- a/tensorrt_llm/_torch/auto_deploy/models/hf.py
+++ b/tensorrt_llm/_torch/auto_deploy/models/hf.py
@@ -121,7 +121,7 @@ class AutoModelForCausalLMFactory(AutoModelFactory):
         self.tokenizer_kwargs = deep_merge_dicts(self._tokenizer_defaults, self.tokenizer_kwargs)
         self.model_kwargs = deep_merge_dicts(
             self._model_defaults,
-            self.model_kwargs,
+            self.model_kwargs or {},
         )
 
         # set sharding config source to huggingface
diff --git a/tensorrt_llm/_torch/model_config.py b/tensorrt_llm/_torch/model_config.py
index 2fff7e47eb..19ed1f3510 100644
--- a/tensorrt_llm/_torch/model_config.py
+++ b/tensorrt_llm/_torch/model_config.py
@@ -4,7 +4,7 @@ import os
 import tempfile
 from dataclasses import dataclass, field
 from pathlib import Path
-from typing import Dict, Generic, List, Optional, TypeVar
+from typing import Any, Dict, Generic, List, Optional, TypeVar
 
 import filelock
 import torch
@@ -470,6 +470,56 @@ class ModelConfig(Generic[TConfig]):
         # Some checkpoints lack torch_dtype, populate with dtype
         pretrained_config.torch_dtype = getattr(pretrained_config, 'dtype',
                                                 None)
+
+        # Apply model_kwargs to override config parameters if provided
+        model_kwargs = kwargs.pop('model_kwargs', None)
+        if model_kwargs:
+
+            def _recursive_update_config(config: transformers.PretrainedConfig,
+                                         update_dict: Dict[str, Any]):
+                """
+                Recursively update a PretrainedConfig object with values from update_dict.
+                Args:
+                    config: PretrainedConfig object to update
+                    update_dict: Dictionary with values to update in the config
+                """
+                for key, value_new in update_dict.items():
+                    if not hasattr(config, key):
+                        logger.warning(
+                            f"model_kwargs key '{key}' not found in pretrained_config, ignoring."
+                        )
+                        continue
+
+                    target_value = getattr(config, key)
+
+                    # Handle nested PretrainedConfig objects when value is a dict
+                    if isinstance(value_new, dict) and isinstance(
+                            target_value, transformers.PretrainedConfig):
+                        # Recursively update the nested config
+                        logger.info(
+                            f"Recursively updating nested config: {key}")
+                        _recursive_update_config(target_value, value_new)
+                    elif (key in ["torch_dtype", "dtype"]
+                          and isinstance(value_new, str)
+                          and value_new != "auto"):
+                        # check special handling of torch_dtype (DEPRECATED!) and dtype keys to ensure we
+                        # use the correct torch.dtype object instead of a string.
+                        dtype = getattr(torch, value_new)
+                        assert isinstance(dtype,
+                                          torch.dtype), f"Invalid {dtype=}"
+                        setattr(config, key, dtype)
+                        logger.info(
+                            f"Applied model_kwargs: {key}={dtype} (previous value: {target_value})"
+                        )
+                    else:
+                        # Direct update for simple values
+                        setattr(config, key, value_new)
+                        logger.info(
+                            f"Applied model_kwargs: {key}={value_new} (previous value: {target_value})"
+                        )
+
+            _recursive_update_config(pretrained_config, model_kwargs)
+
         quant_config = QuantConfig()
         layer_quant_config = None
         moe_backend = kwargs.get('moe_backend', 'CUTLASS')
diff --git a/tensorrt_llm/_torch/models/checkpoints/mistral/config_loader.py b/tensorrt_llm/_torch/models/checkpoints/mistral/config_loader.py
index c679734fcf..dbc7abf730 100644
--- a/tensorrt_llm/_torch/models/checkpoints/mistral/config_loader.py
+++ b/tensorrt_llm/_torch/models/checkpoints/mistral/config_loader.py
@@ -8,6 +8,7 @@ from transformers import PretrainedConfig, WhisperConfig
 from tensorrt_llm._torch.model_config import ModelConfig
 from tensorrt_llm._torch.models.checkpoints.base_config_loader import BaseConfigLoader
 from tensorrt_llm._torch.models.modeling_utils import register_config_loader
+from tensorrt_llm.logger import logger
 from tensorrt_llm.models.modeling_utils import QuantConfig
 from tensorrt_llm.quantization.mode import QuantAlgo
 
@@ -327,6 +328,15 @@ class MistralConfigLoader(BaseConfigLoader):
                     block_size = (128, 128)
                 quant_config.group_size = block_size[0]
 
+        # model_kwargs is not supported for Mistral format checkpoints
+        # Extract it from kwargs to avoid passing to ModelConfig.__init__ (which doesn't accept it)
+        model_kwargs = kwargs.pop("model_kwargs", None)
+        if model_kwargs:
+            logger.warning(
+                "model_kwargs is not supported for Mistral format checkpoints. "
+                f"Ignoring model_kwargs: {model_kwargs}"
+            )
+
         kwargs.pop("trust_remote_code", None)  # ModelConfig does not have this input parameter
         model_config = ModelConfig(
             pretrained_config=pretrained_config,
diff --git a/tensorrt_llm/_torch/pyexecutor/model_loader.py b/tensorrt_llm/_torch/pyexecutor/model_loader.py
index 4756e24d08..1d24d24924 100644
--- a/tensorrt_llm/_torch/pyexecutor/model_loader.py
+++ b/tensorrt_llm/_torch/pyexecutor/model_loader.py
@@ -338,8 +338,8 @@ class ModelLoader:
             self, checkpoint_dir: str,
             checkpoint_loader: BaseCheckpointLoader) -> ModelConfig:
         """Loads and validates the model configuration."""
-        config = checkpoint_loader.load_config(
-            checkpoint_dir,
+        load_config_kwargs = dict(
+            checkpoint_dir=checkpoint_dir,
             trust_remote_code=True,
             mapping=self.mapping,
             enable_min_latency=self.llm_args.enable_min_latency,
@@ -363,6 +363,12 @@ class ModelLoader:
             nvfp4_gemm_allowed_backends=self.llm_args.nvfp4_gemm_config.
             allowed_backends)
 
+        # Only pass model_kwargs if it's explicitly set (not None)
+        if self.llm_args.model_kwargs is not None:
+            load_config_kwargs['model_kwargs'] = self.llm_args.model_kwargs
+
+        config = checkpoint_loader.load_config(**load_config_kwargs)
+
         # Store nvfp4 config in extra_attrs for Linear layer access
         config.extra_attrs[
             'nvfp4_gemm_allowed_backends'] = config.nvfp4_gemm_allowed_backends
@@ -373,9 +379,13 @@ class ModelLoader:
             config, self.llm_args.kv_cache_config.mamba_ssm_cache_dtype)
 
         # Allow overriding the number of layers via environment variable
+        # Note: This is kept for backward compatibility, but model_kwargs is preferred
         num_layers_override = int(os.environ.get("TLLM_OVERRIDE_LAYER_NUM",
                                                  "0"))
         if num_layers_override > 0:
+            logger.warning(
+                f"TLLM_OVERRIDE_LAYER_NUM is deprecated. Use model_kwargs instead: "
+                f"model_kwargs={{'num_hidden_layers': {num_layers_override}}}")
             config.pretrained_config.num_hidden_layers = num_layers_override
             for sub_config in ["text_config", "vision_config"]:
                 if hasattr(config.pretrained_config, sub_config):
diff --git a/tensorrt_llm/llmapi/llm_args.py b/tensorrt_llm/llmapi/llm_args.py
index 3f15252b84..1baae2a8eb 100644
--- a/tensorrt_llm/llmapi/llm_args.py
+++ b/tensorrt_llm/llmapi/llm_args.py
@@ -1907,6 +1907,13 @@ class BaseLlmArgs(StrictBaseModel):
 
     # Below are all remaining arguments
 
+    model_kwargs: Optional[Dict[str, Any]] = Field(
+        default=None,
+        description="Optional parameters overriding model config defaults. "
+        "Precedence: (1) model_kwargs, (2) model config file, (3) model config class defaults. "
+        "Unknown keys are ignored",
+        status="prototype")
+
     pipeline_parallel_size: int = Field(
         default=1, description="The pipeline parallel size.")
 
diff --git a/tests/unittest/api_stability/references/llm.yaml b/tests/unittest/api_stability/references/llm.yaml
index 4b6f8cedab..1c261c55fc 100644
--- a/tests/unittest/api_stability/references/llm.yaml
+++ b/tests/unittest/api_stability/references/llm.yaml
@@ -227,6 +227,10 @@ methods:
         annotation: Optional[Dict[str, str]]
         default: null
         status: prototype
+      model_kwargs:
+        annotation: Optional[Dict[str, Any]]
+        default: null
+        status: prototype
     return_annotation: None
   generate:
     parameters:
diff --git a/tests/unittest/llmapi/test_llm_args.py b/tests/unittest/llmapi/test_llm_args.py
index 55c6c7b055..b5c74bc8e7 100644
--- a/tests/unittest/llmapi/test_llm_args.py
+++ b/tests/unittest/llmapi/test_llm_args.py
@@ -138,6 +138,19 @@ max_seq_len: 128
         assert llm_args.max_num_tokens == 256
         assert llm_args.max_seq_len == 128
 
+    @pytest.mark.parametrize("llm_args_cls", [TrtLlmArgs, TorchLlmArgs])
+    def test_llm_args_with_model_kwargs(self, llm_args_cls):
+        yaml_content = """
+model_kwargs:
+    num_hidden_layers: 2
+    """
+        dict_content = self._yaml_to_dict(yaml_content)
+        llm_args = llm_args_cls(model=llama_model_path)
+        llm_args_dict = update_llm_args_with_extra_dict(llm_args.model_dump(),
+                                                        dict_content)
+        llm_args = llm_args_cls(**llm_args_dict)
+        assert llm_args.model_kwargs['num_hidden_layers'] == 2
+
 
 def check_defaults(py_config_cls, pybind_config_cls):
     py_config = py_config_cls()
@@ -445,6 +458,18 @@ class TestTorchLlmArgs:
             args = TorchLlmArgs(model=llama_model_path)
             args.invalid_arg = 1
 
+    @print_traceback_on_error
+    def test_model_kwargs_with_num_hidden_layers(self):
+        """Test that model_kwargs can override num_hidden_layers."""
+        from tensorrt_llm._torch.model_config import ModelConfig
+        config_no_kwargs = ModelConfig.from_pretrained(
+            llama_model_path).pretrained_config
+        model_kwargs = {'num_hidden_layers': 2}
+        config_with_kwargs = ModelConfig.from_pretrained(
+            llama_model_path, model_kwargs=model_kwargs).pretrained_config
+        assert config_no_kwargs.num_hidden_layers != config_with_kwargs.num_hidden_layers
+        assert config_with_kwargs.num_hidden_layers == 2
+
 
 class TestTrtLlmArgs: