diff --git a/sdata/subcmd-install/3.files-exp.yaml b/sdata/subcmd-install/3.files-exp.yaml
index 5282e0594..63a0cad1f 100644
--- a/sdata/subcmd-install/3.files-exp.yaml
+++ b/sdata/subcmd-install/3.files-exp.yaml
@@ -20,6 +20,7 @@ patterns:
   - from: "dots/.config/fish"
     to: "$XDG_CONFIG_HOME/fish"
     mode: "sync"
+    excludes: ["conf.d"]
     condition:
       type: "shell"
       value: "fish"
diff --git a/sdata/subcmd-install/3.files-legacy.sh b/sdata/subcmd-install/3.files-legacy.sh
index 6ba8cefc2..98d792be8 100644
--- a/sdata/subcmd-install/3.files-legacy.sh
+++ b/sdata/subcmd-install/3.files-legacy.sh
@@ -30,7 +30,11 @@ esac
 case "${SKIP_FISH}" in
   true) sleep 0;;
   *)
-    install_dir__sync dots/.config/fish "$XDG_CONFIG_HOME"/fish
+    # Use rsync with exclude to preserve user's custom conf.d directory
+    if [ -d "$XDG_CONFIG_HOME"/fish ];then
+      warning_overwrite
+    fi
+    rsync_dir__sync_exclude dots/.config/fish "$XDG_CONFIG_HOME"/fish "conf.d"
     ;;
 esac
 
diff --git a/sdata/subcmd-install/3.files.sh b/sdata/subcmd-install/3.files.sh
index 41e9972d0..49490a49f 100644
--- a/sdata/subcmd-install/3.files.sh
+++ b/sdata/subcmd-install/3.files.sh
@@ -67,6 +67,22 @@ rsync_dir__sync(){
   x mkdir -p "$(dirname ${INSTALLED_LISTFILE})"
   rsync -a --delete --out-format='%i %n' "$1"/ "$2"/ | awk -v d="$dest" '$1 ~ /^>/{ sub(/^[^ ]+ /,""); printf d "/" $0 "\n" }' >> "${INSTALLED_LISTFILE}"
 }
+rsync_dir__sync_exclude(){
+  # NOTE: This function is only for using in other functions
+  # Same as rsync_dir__sync but with exclude patterns support
+  # Usage: rsync_dir__sync_exclude <src> <dest> <exclude_pattern1> [<exclude_pattern2> ...]
+  local src="$1"
+  local dest_dir="$2"
+  shift 2
+  local excludes=()
+  for pattern in "$@"; do
+    excludes+=(--exclude "$pattern")
+  done
+  x mkdir -p "$dest_dir"
+  local dest="$(realpath -se $dest_dir)"
+  x mkdir -p "$(dirname ${INSTALLED_LISTFILE})"
+  rsync -a --delete "${excludes[@]}" --out-format='%i %n' "$src"/ "$dest_dir"/ | awk -v d="$dest" '$1 ~ /^>/{ sub(/^[^ ]+ /,""); printf d "/" $0 "\n" }' >> "${INSTALLED_LISTFILE}"
+}
 function install_file(){
   # NOTE: Do not add prefix `v` or `x` when using this function
   local s=$1