diff --git a/doc/_static/css/custom.css b/doc/_static/css/custom.css
index d0b761e71d..8bcfdd3c7e 100644
--- a/doc/_static/css/custom.css
+++ b/doc/_static/css/custom.css
@@ -11,7 +11,7 @@ pre {
 img.platform-icon {
   height: 2ex;
 }
-@media (prefers-color-scheme: dark) {
+html[data-theme="dark"] {
   .wy-side-nav-search .wy-dropdown > a img.logo,
   .wy-side-nav-search > a img.logo {
     content: url("../logo-dark.svg");
diff --git a/doc/conf.py b/doc/conf.py
index 51d463fd1f..c72e05bf8a 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -44,7 +44,7 @@
 # ones.
 # extensions = [
 #     'recommonmark',
-#     "sphinx_rtd_theme",
+#     "sphinx_book_theme",
 #     'myst_parser',
 #     'sphinx_markdown_tables',
 #     'sphinx.ext.autosummary'
@@ -53,7 +53,7 @@
 extensions = [
     "deepmodeling_sphinx",
     "dargs.sphinx",
-    "sphinx_rtd_theme",
+    "sphinx_book_theme",
     "myst_nb",
     "sphinx.ext.autosummary",
     "sphinx.ext.mathjax",
@@ -70,6 +70,7 @@
     "autoapi.extension",
     "sphinxcontrib.programoutput",
     "sphinxcontrib.moderncmakedomain",
+    "sphinx_remove_toctrees",
 ]
 
 # breathe_domain_by_extension = {
@@ -175,9 +176,15 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "sphinx_rtd_theme"
+html_theme = "sphinx_book_theme"
 html_logo = "_static/logo.svg"
 
+html_theme_options = {
+    "logo": {
+        "image_light": "_static/logo.svg",
+        "image_dark": "_static/logo-dark.svg",
+    }
+}
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
@@ -215,3 +222,5 @@
 napoleon_numpy_docstring = False
 
 bibtex_bibfiles = ["../CITATIONS.bib"]
+
+remove_from_toctrees = ["autoapi/**/*", "API_CC/*", "api_c/*", "api_core/*"]
diff --git a/pyproject.toml b/pyproject.toml
index 6f0404174d..00f83fef06 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -89,7 +89,7 @@ test = [
 ]
 docs = [
     "sphinx>=3.1.1",
-    "sphinx_rtd_theme>=1.0.0rc1",
+    "sphinx-book-theme",
     "myst-nb>=1.0.0rc0",
     "myst-parser>=0.19.2",
     "sphinx-design",
@@ -97,7 +97,7 @@ docs = [
     "exhale>=0.3.7",
     "numpydoc",
     "ase",
-    "deepmodeling-sphinx>=0.1.0",
+    "deepmodeling-sphinx>=0.3.0",
     "dargs>=0.3.4",
     "sphinx-argparse<0.5.0",
     "pygments-lammps",
@@ -105,6 +105,7 @@ docs = [
     "sphinx-autoapi>=3.0.0",
     "sphinxcontrib-programoutput",
     "sphinxcontrib-moderncmakedomain",
+    "sphinx-remove-toctrees",
 ]
 lmp = [
     "lammps~=2024.8.29.1.0",