diff --git a/xmake/plugins/project/clang/compile_commands.lua b/xmake/plugins/project/clang/compile_commands.lua
index 9435819df7d..a017b4a32bf 100644
--- a/xmake/plugins/project/clang/compile_commands.lua
+++ b/xmake/plugins/project/clang/compile_commands.lua
@@ -308,6 +308,7 @@ function make(outputdir)
     local oldir = os.cd(os.projectdir())
     local jsonfile = io.open(path.join(outputdir, "compile_commands.json"), "w")
     os.setenv("XMAKE_IN_COMPILE_COMMANDS_PROJECT_GENERATOR", "true")
+    target_cmds.prepare_targets()
     _add_targets(jsonfile)
     jsonfile:close()
     os.setenv("XMAKE_IN_COMPILE_COMMANDS_PROJECT_GENERATOR", nil)
diff --git a/xmake/plugins/project/clang/compile_flags.lua b/xmake/plugins/project/clang/compile_flags.lua
index e4b07ec340b..07f9de38c7e 100644
--- a/xmake/plugins/project/clang/compile_flags.lua
+++ b/xmake/plugins/project/clang/compile_flags.lua
@@ -23,6 +23,7 @@ import("core.tool.compiler")
 import("core.project.project")
 import("core.language.language")
 import("private.utils.target", {alias = "target_utils"})
+import("plugins.project.utils.target_cmds", {rootdir = os.programdir()})
 
 -- make the object
 function _make_object(target, flags, sourcefile, objectfile)
diff --git a/xmake/rules/c++/precompiled_header/xmake.lua b/xmake/rules/c++/precompiled_header/xmake.lua
index dc6fcb27e01..a2b08fe46a2 100644
--- a/xmake/rules/c++/precompiled_header/xmake.lua
+++ b/xmake/rules/c++/precompiled_header/xmake.lua
@@ -23,7 +23,9 @@ rule("c.build.pcheader")
         import("private.action.build.pcheader").config(target, "c", opt)
     end)
     before_prepare(function (target, jobgraph, opt)
-        import("private.action.build.pcheader").build(target, jobgraph, "c", opt)
+        if not os.getenv("XMAKE_IN_COMPILE_COMMANDS_PROJECT_GENERATOR") then
+            import("private.action.build.pcheader").build(target, jobgraph, "c", opt)
+        end
     end, {jobgraph = true})
 
 rule("c++.build.pcheader")
@@ -32,6 +34,8 @@ rule("c++.build.pcheader")
         import("private.action.build.pcheader").config(target, "cxx", opt)
     end)
     before_prepare(function (target, jobgraph, opt)
-        import("private.action.build.pcheader").build(target, jobgraph, "cxx", opt)
+        if not os.getenv("XMAKE_IN_COMPILE_COMMANDS_PROJECT_GENERATOR") then
+            import("private.action.build.pcheader").build(target, jobgraph, "cxx", opt)
+        end
     end, {jobgraph = true})