diff --git a/.flake8 b/.flake8
index 853e887f5e40ac9aa2d61fa88d4e810a50c6cc81..3828a989ebe6f13992bc3cb997517e0791cf37ce 100644
--- a/.flake8
+++ b/.flake8
@@ -6,8 +6,6 @@ exclude =
     # https://github.com/PaddlePaddle/Paddle/pull/46290#discussion_r976392010
     ./python/paddle/fluid/[!t]**,
     ./python/paddle/fluid/tra**,
-    # Exclude auto-generated files
-    *_pb2.py,
     # Exclude third-party libraries
     ./python/paddle/utils/gast/**,
     # Exclude files that will be removed in the future, see more at
@@ -15,18 +13,16 @@ exclude =
     ./python/paddle/fluid/tests/unittests/npu/**,
     ./python/paddle/fluid/tests/unittests/mlu/**
 ignore =
-    # E, see https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes
-    E203,
-    E402,
-    E501,
-    E721,E722,E731,E741,
-
-    # F, see https://flake8.pycqa.org/en/latest/user/error-codes.html
-    F405,
-    F841,
-
-    # W, see https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes
-    W503
+    E203, # Whitespace before ‘,’, ‘;’, or ‘:’, it is not compatible with black
+    E402, # Module level import not at top of file
+    E501, # Line too long (82 > 79 characters)
+    E721, # Do not compare types, use `isinstance()`
+    E722, # Do not use bare except, specify exception instead
+    E731, # Do not assign a lambda expression, use a def
+    E741, # Do not use variables named ‘l’, ‘O’, or ‘I’
+    F405, # `name` may be undefined, or defined from star imports: `module`
+    F841, # Local variable name is assigned to but never used
+    W503  # Line break before binary operator, it is not compatible with black
 per-file-ignores =
     # These files need tabs for testing.
     python/paddle/fluid/tests/unittests/dygraph_to_static/test_error.py:E101,W191
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 816882418964313e8062ef14a7bc108e63dcaf78..d28d5adae30862e1641c0ffe70ce511b61efa5fa 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -5,7 +5,6 @@ exclude: |
         paddle/fluid/framework/fleet/heter_ps/cudf/.+|
         paddle/fluid/distributed/ps/thirdparty/round_robin.h|
         python/paddle/utils/gast/.+|
-        .+_pb2\.py|
         python/paddle/fluid/tests/unittests/npu/.+|
         python/paddle/fluid/tests/unittests/mlu/.+
     )$
diff --git a/pyproject.toml b/pyproject.toml
index 6bcec760a6c65a429ba766b4ce010538405fdc78..d42ee7ab0ec5408bd2c8a0014dd388f9f68fb657 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,7 +13,6 @@ extend_skip_glob = [
     # see .flake8 for more details
     "python/paddle/fluid/[!t]**",
     "python/paddle/fluid/tra**",
-    "*_pb2.py",
     "python/paddle/utils/gast/**",
     "python/paddle/fluid/tests/unittests/npu/**",
     "python/paddle/fluid/tests/unittests/mlu/**",