diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1245f1b4cb1d8..ccf1db464d344 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -68,16 +68,6 @@ repos:
     hooks:
     -   id: flake8
         args: ["--config=.flake8"]
--   repo: https://github.com/PyCQA/autoflake
-    rev: v1.7.7
-    hooks:
-    -   id: autoflake
-        args:
-            - --in-place
-            - --remove-all-unused-imports
-            - --ignore-pass-after-docstring
-            - --ignore-init-module-imports
-            - --exclude=python/paddle/fluid/[!t]**,python/paddle/fluid/tra**
 -   repo: https://github.com/charliermarsh/ruff-pre-commit
     rev: v0.0.254
     hooks:
diff --git a/pyproject.toml b/pyproject.toml
index cf4afca27c328..f244f6c1d45e4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,6 +29,9 @@ exclude = [
 ]
 target-version = "py37"
 select = [
+    # Pyflakes
+    "F401",
+
     # Pyupgrade
     "UP001",
     "UP003",