diff --git a/source/module_esolver/esolver_ks_lcao.cpp b/source/module_esolver/esolver_ks_lcao.cpp
index da425394f0..554be9a3c0 100644
--- a/source/module_esolver/esolver_ks_lcao.cpp
+++ b/source/module_esolver/esolver_ks_lcao.cpp
@@ -185,7 +185,11 @@ void ESolver_KS_LCAO<TK, TR>::before_all_runners(UnitCell& ucell, const Input_pa
     {
         if (GlobalC::exx_info.info_global.cal_exx)
         {
-            XC_Functional::set_xc_first_loop(ucell);
+            if (PARAM.inp.init_wfc != "file")
+            {   // if init_wfc==file, directly enter the EXX loop
+                XC_Functional::set_xc_first_loop(ucell);
+            }
+
             // initialize 2-center radial tables for EXX-LRI
             if (GlobalC::exx_info.info_ri.real_number)
             {
@@ -607,7 +611,17 @@ void ESolver_KS_LCAO<TK, TR>::iter_init(UnitCell& ucell, const int istep, const
     // electrons number.
     if (istep == 0 && PARAM.inp.init_wfc == "file")
     {
-        if (iter == 1)
+        int exx_two_level_step = 0;
+#ifdef __EXX
+        if (GlobalC::exx_info.info_global.cal_exx)
+        {
+            // the following steps are only needed in the first outer exx loop
+            exx_two_level_step = GlobalC::exx_info.info_ri.real_number ?
+                this->exd->two_level_step
+                : this->exc->two_level_step;
+        }
+#endif 
+        if (iter == 1 && exx_two_level_step == 0)
         {
             std::cout << " WAVEFUN -> CHARGE " << std::endl;
 
diff --git a/source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/op_exx_lcao.hpp b/source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/op_exx_lcao.hpp
index e20ca09b6e..5c4af43f40 100644
--- a/source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/op_exx_lcao.hpp
+++ b/source/module_hamilt_lcao/hamilt_lcaodft/operator_lcao/op_exx_lcao.hpp
@@ -251,7 +251,14 @@ void OperatorEXX<OperatorLCAO<TK, TR>>::contributeHR()
 {
     ModuleBase::TITLE("OperatorEXX", "contributeHR");
     // Peize Lin add 2016-12-03
-    if (this->istep == 0 && PARAM.inp.calculation != "nscf" && this->two_level_step != nullptr && *this->two_level_step == 0 && !this->restart) { return; }  //in the non-exx loop, do nothing 
+    if (this->istep == 0
+        && PARAM.inp.calculation != "nscf"
+        && this->two_level_step != nullptr && *this->two_level_step == 0
+        && PARAM.inp.init_wfc != "file"
+        && !this->restart)
+    {
+        return;
+    }  //in the non-exx loop, do nothing 
     if (this->add_hexx_type == Add_Hexx_Type::k) { return; }
 
     if (XC_Functional::get_func_type() == 4 || XC_Functional::get_func_type() == 5)
diff --git a/source/module_ri/Exx_LRI_interface.hpp b/source/module_ri/Exx_LRI_interface.hpp
index cdf3b219c9..8eecf44cc9 100644
--- a/source/module_ri/Exx_LRI_interface.hpp
+++ b/source/module_ri/Exx_LRI_interface.hpp
@@ -62,10 +62,12 @@ void Exx_LRI_Interface<T, Tdata>::exx_beforescf(const int istep,
 #ifdef __MPI
     if (GlobalC::exx_info.info_global.cal_exx)
     {
-        if (GlobalC::restart.info_load.load_H_finish && !GlobalC::restart.info_load.restart_exx) { XC_Functional::set_xc_type(ucell.atoms[0].ncpp.xc_func);
-        } 
-        else if (istep > 0) { XC_Functional::set_xc_type(ucell.atoms[0].ncpp.xc_func);
-        } 
+        if ((GlobalC::restart.info_load.load_H_finish && !GlobalC::restart.info_load.restart_exx)
+            || (istep > 0)
+            || (PARAM.inp.init_wfc == "file"))
+        {
+            XC_Functional::set_xc_type(ucell.atoms[0].ncpp.xc_func);
+        }
         else
         {
             if (ucell.atoms[0].ncpp.xc_func == "HF" || ucell.atoms[0].ncpp.xc_func == "PBE0" || ucell.atoms[0].ncpp.xc_func == "HSE")
@@ -120,10 +122,13 @@ void Exx_LRI_Interface<T, Tdata>::exx_eachiterinit(const int istep,
                                                    const K_Vectors& kv, 
                                                    const int& iter)
 {
+    std::cout << "iter=" << iter << std::endl;
     if (GlobalC::exx_info.info_global.cal_exx)
     {
-        if (!GlobalC::exx_info.info_global.separate_loop && (this->two_level_step || istep > 0))
+        if (!GlobalC::exx_info.info_global.separate_loop && (this->two_level_step || istep > 0 || PARAM.inp.init_wfc == "file") // non separate loop case
+            || (GlobalC::exx_info.info_global.separate_loop && PARAM.inp.init_wfc == "file" && this->two_level_step == 0 && iter == 1))  // the first iter in separate loop case
         {
+            std::cout << "update exx" << std::endl;
             const bool flag_restart = (iter == 1) ? true : false;
             auto cal = [this, &ucell,&kv, &flag_restart](const elecstate::DensityMatrix<T, double>& dm_in)
             {
@@ -313,7 +318,8 @@ bool Exx_LRI_Interface<T, Tdata>::exx_after_converge(
                 std::cout << " Updating EXX " << std::flush;
                 timeval t_start;       gettimeofday(&t_start, nullptr);
 
-                const bool flag_restart = (this->two_level_step == 0) ? true : false;
+                // if init_wfc == "file", DM is calculated in the 1st iter of the 1st two-level step, so we mix it here
+                const bool flag_restart = (this->two_level_step == 0 && PARAM.inp.init_wfc != "file") ? true : false;
 
                 if (this->exx_spacegroup_symmetry)
                     {this->mix_DMk_2D.mix(symrot_.restore_dm(kv, dm.get_DMK_vector(), *dm.get_paraV_pointer()), flag_restart);}