diff --git a/.gitignore b/.gitignore
index dbcf687197..e9b29e2382 100644
--- a/.gitignore
+++ b/.gitignore
@@ -27,7 +27,8 @@ venv*
 _build
 _templates
 API_CC
+doc/api_py/
 dp/
 build_lammps/
 build_tests/
-build_cc_tests
\ No newline at end of file
+build_cc_tests
diff --git a/doc/conf.py b/doc/conf.py
index 0dfac83f24..f7515cb7b3 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -130,10 +130,19 @@ def generate_doxygen_xml(app):
     else:
         subprocess.call("doxygen Doxyfile", shell=True)
 
+def run_apidoc(_):
+    from sphinx.ext.apidoc import main
+    import sys
+    sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
+    cur_dir = os.path.abspath(os.path.dirname(__file__))
+    module = os.path.join(cur_dir,"..","deepmd")
+    main(['-M', '--tocfile', 'api_py', '-H', 'Python API', '-o', os.path.join(cur_dir, "api_py"), module, '--force'])
+
 def setup(app):
 
     # Add hook for building doxygen xml when needed
     app.connect("builder-inited", generate_doxygen_xml)
+    app.connect('builder-inited', run_apidoc)
 
 # -- General configuration ---------------------------------------------------
 
@@ -158,6 +167,7 @@ def setup(app):
     'sphinx.ext.autosummary',
     'sphinx.ext.viewcode',
     'sphinx.ext.intersphinx',
+    'numpydoc',
     'breathe',
     'exhale'
 ]
@@ -184,10 +194,10 @@ def setup(app):
 }
 
 # Tell sphinx what the primary language being documented is.
-primary_domain = 'cpp'
+#primary_domain = 'cpp'
 
 # Tell sphinx what the pygments highlight language should be.
-highlight_language = 'cpp'
+#highlight_language = 'cpp'
 
 # 
 myst_heading_anchors = 4
@@ -206,7 +216,8 @@ def setup(app):
     "tensorflow": (
         "https://www.tensorflow.org/api_docs/python",
         "https://github.com/mr-ubik/tensorflow-intersphinx/raw/master/tf2_py_objects.inv",
-    ),
+    ), 
+    "ase": ("https://wiki.fysik.dtu.dk/ase/", None),
 }
 
 # -- Options for HTML output -------------------------------------------------
diff --git a/doc/development/api.rst b/doc/development/api.rst
deleted file mode 100644
index eda136f00e..0000000000
--- a/doc/development/api.rst
+++ /dev/null
@@ -1,123 +0,0 @@
-Python API
-==========
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-
-.. automodule:: deepmd.utils.data
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.infer.data_modifier
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.utils.data_system
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.infer.deep_eval
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.infer.deep_polar
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.infer.deep_pot
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.infer.deep_wfc
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.descriptor.loc_frame
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.descriptor.se_a
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.descriptor.se_r
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.descriptor.se_ar
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.descriptor.se_a_ebd
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.descriptor.se_t
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.descriptor.se_a_ef
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.descriptor.hybrid
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.infer.ewald_recp
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.fit.ener
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.fit.dipole
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.fit.polar
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.fit.wfc
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.utils.network
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.utils.learning_rate
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.cluster.local
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.cluster.slurm
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.loss.ener
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.loss.tensor
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.model.ener
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.model.tensor
-   :members:
-   :undoc-members:
-
-.. automodule:: deepmd.train.trainer
-   :members:
-   :undoc-members:
-
diff --git a/doc/index.rst b/doc/index.rst
index 7cd8968f01..2b6cf74fbf 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -39,11 +39,12 @@ DeePMD-kit is a package written in Python/C++, designed to minimize the effort r
 .. _developer-guide:
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 5
    :caption: Developer Guide
    :glob:
 
    development/*
+   api_py/api_py
    API_CC/api_cc
 
 
diff --git a/setup.py b/setup.py
index e48f9a3f3d..35ef146879 100644
--- a/setup.py
+++ b/setup.py
@@ -125,7 +125,7 @@
     cmake_minimum_required_version="3.0",
     extras_require={
         "test": ["dpdata>=0.1.9", "ase", "pytest", "pytest-cov", "pytest-sugar"],
-        "docs": ["sphinx<4.1.0", "recommonmark", "sphinx_rtd_theme", "sphinx_markdown_tables", "myst-parser", "breathe", "exhale"],
+        "docs": ["sphinx>=3.1.1,<4.1.0", "recommonmark", "sphinx_rtd_theme", "sphinx_markdown_tables", "myst-parser", "breathe", "exhale", "numpydoc", "ase"],
         **extras_require,
     },
     entry_points={"console_scripts": ["dp = deepmd.entrypoints.main:main"]},