diff --git a/fe/fe-core/src/main/java/org/apache/doris/nereids/parser/LogicalPlanBuilder.java b/fe/fe-core/src/main/java/org/apache/doris/nereids/parser/LogicalPlanBuilder.java
index 07d6f77f6d0f8c..4a80e98a506f42 100644
--- a/fe/fe-core/src/main/java/org/apache/doris/nereids/parser/LogicalPlanBuilder.java
+++ b/fe/fe-core/src/main/java/org/apache/doris/nereids/parser/LogicalPlanBuilder.java
@@ -1834,7 +1834,9 @@ private LogicalPlan withSelectHint(LogicalPlan logicalPlan, List<ParserRuleConte
                                 parameters.put(parameterName, value);
                             }
                         }
-                        hints.put(hintName, new SelectHintSetVar(hintName, parameters));
+                        SelectHintSetVar setVar = new SelectHintSetVar(hintName, parameters);
+                        setVar.setVarOnceInSql(ConnectContext.get().getStatementContext());
+                        hints.put(hintName, setVar);
                         break;
                     case "leading":
                         List<String> leadingParameters = new ArrayList<String>();
diff --git a/fe/fe-core/src/main/java/org/apache/doris/nereids/properties/SelectHintSetVar.java b/fe/fe-core/src/main/java/org/apache/doris/nereids/properties/SelectHintSetVar.java
index 8c08dcf378fabd..0d54cb75b1e6cc 100644
--- a/fe/fe-core/src/main/java/org/apache/doris/nereids/properties/SelectHintSetVar.java
+++ b/fe/fe-core/src/main/java/org/apache/doris/nereids/properties/SelectHintSetVar.java
@@ -17,6 +17,13 @@
 
 package org.apache.doris.nereids.properties;
 
+import org.apache.doris.analysis.SetVar;
+import org.apache.doris.analysis.StringLiteral;
+import org.apache.doris.nereids.StatementContext;
+import org.apache.doris.nereids.exceptions.AnalysisException;
+import org.apache.doris.qe.SessionVariable;
+import org.apache.doris.qe.VariableMgr;
+
 import java.util.Map;
 import java.util.Optional;
 import java.util.stream.Collectors;
@@ -38,6 +45,42 @@ public Map<String, Optional<String>> getParameters() {
         return parameters;
     }
 
+    /**
+     * set session variable in sql level
+     * @param context statement context
+     */
+    public void setVarOnceInSql(StatementContext context) {
+        if (context == null) {
+            return;
+        }
+        SessionVariable sessionVariable = context.getConnectContext().getSessionVariable();
+        // set temporary session value, and then revert value in the 'finally block' of StmtExecutor#execute
+        sessionVariable.setIsSingleSetVar(true);
+        for (Map.Entry<String, Optional<String>> kv : getParameters().entrySet()) {
+            String key = kv.getKey();
+            Optional<String> value = kv.getValue();
+            if (value.isPresent()) {
+                try {
+                    VariableMgr.setVar(sessionVariable, new SetVar(key, new StringLiteral(value.get())));
+                } catch (Throwable t) {
+                    throw new AnalysisException("Can not set session variable '"
+                        + key + "' = '" + value.get() + "'", t);
+                }
+            }
+        }
+        // if sv set enable_nereids_planner=true and hint set enable_nereids_planner=false, we should set
+        // enable_fallback_to_original_planner=true and revert it after executing.
+        // throw exception to fall back to original planner
+        if (!sessionVariable.isEnableNereidsPlanner()) {
+            try {
+                sessionVariable.enableFallbackToOriginalPlannerOnce();
+            } catch (Throwable t) {
+                throw new AnalysisException("failed to set fallback to original planner to true", t);
+            }
+            throw new AnalysisException("The nereids is disabled in this sql, fallback to original planner");
+        }
+    }
+
     @Override
     public String toString() {
         String kvString = parameters
diff --git a/fe/fe-core/src/main/java/org/apache/doris/nereids/rules/analysis/EliminateLogicalSelectHint.java b/fe/fe-core/src/main/java/org/apache/doris/nereids/rules/analysis/EliminateLogicalSelectHint.java
index 06d85e660b090a..295a5ebb0a066b 100644
--- a/fe/fe-core/src/main/java/org/apache/doris/nereids/rules/analysis/EliminateLogicalSelectHint.java
+++ b/fe/fe-core/src/main/java/org/apache/doris/nereids/rules/analysis/EliminateLogicalSelectHint.java
@@ -17,12 +17,9 @@
 
 package org.apache.doris.nereids.rules.analysis;
 
-import org.apache.doris.analysis.SetVar;
-import org.apache.doris.analysis.StringLiteral;
 import org.apache.doris.common.DdlException;
 import org.apache.doris.nereids.CascadesContext;
 import org.apache.doris.nereids.StatementContext;
-import org.apache.doris.nereids.exceptions.AnalysisException;
 import org.apache.doris.nereids.hint.Hint;
 import org.apache.doris.nereids.hint.LeadingHint;
 import org.apache.doris.nereids.hint.OrderedHint;
@@ -35,15 +32,12 @@
 import org.apache.doris.nereids.trees.plans.Plan;
 import org.apache.doris.nereids.trees.plans.logical.LogicalSelectHint;
 import org.apache.doris.qe.ConnectContext;
-import org.apache.doris.qe.SessionVariable;
-import org.apache.doris.qe.VariableMgr;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.util.Map;
 import java.util.Map.Entry;
-import java.util.Optional;
 
 /**
  * eliminate logical select hint and set them to cascade context
@@ -58,7 +52,7 @@ public Rule build() {
             for (Entry<String, SelectHint> hint : selectHintPlan.getHints().entrySet()) {
                 String hintName = hint.getKey();
                 if (hintName.equalsIgnoreCase("SET_VAR")) {
-                    setVar((SelectHintSetVar) hint.getValue(), ctx.statementContext);
+                    ((SelectHintSetVar) hint.getValue()).setVarOnceInSql(ctx.statementContext);
                 } else if (hintName.equalsIgnoreCase("ORDERED")) {
                     try {
                         ctx.cascadesContext.getConnectContext().getSessionVariable()
@@ -81,35 +75,6 @@ public Rule build() {
         }).toRule(RuleType.ELIMINATE_LOGICAL_SELECT_HINT);
     }
 
-    private void setVar(SelectHintSetVar selectHint, StatementContext context) {
-        SessionVariable sessionVariable = context.getConnectContext().getSessionVariable();
-        // set temporary session value, and then revert value in the 'finally block' of StmtExecutor#execute
-        sessionVariable.setIsSingleSetVar(true);
-        for (Entry<String, Optional<String>> kv : selectHint.getParameters().entrySet()) {
-            String key = kv.getKey();
-            Optional<String> value = kv.getValue();
-            if (value.isPresent()) {
-                try {
-                    VariableMgr.setVar(sessionVariable, new SetVar(key, new StringLiteral(value.get())));
-                } catch (Throwable t) {
-                    throw new AnalysisException("Can not set session variable '"
-                        + key + "' = '" + value.get() + "'", t);
-                }
-            }
-        }
-        // if sv set enable_nereids_planner=true and hint set enable_nereids_planner=false, we should set
-        // enable_fallback_to_original_planner=true and revert it after executing.
-        // throw exception to fall back to original planner
-        if (!sessionVariable.isEnableNereidsPlanner()) {
-            try {
-                sessionVariable.enableFallbackToOriginalPlannerOnce();
-            } catch (Throwable t) {
-                throw new AnalysisException("failed to set fallback to original planner to true", t);
-            }
-            throw new AnalysisException("The nereids is disabled in this sql, fallback to original planner");
-        }
-    }
-
     private void extractLeading(SelectHintLeading selectHint, CascadesContext context,
                                     StatementContext statementContext, Map<String, SelectHint> hints) {
         LeadingHint hint = new LeadingHint("Leading", selectHint.getParameters(), selectHint.toString());
diff --git a/fe/fe-core/src/test/java/org/apache/doris/qe/SessionVariablesTest.java b/fe/fe-core/src/test/java/org/apache/doris/qe/SessionVariablesTest.java
index 2ba2291bc4d8ff..238c2b52ede901 100644
--- a/fe/fe-core/src/test/java/org/apache/doris/qe/SessionVariablesTest.java
+++ b/fe/fe-core/src/test/java/org/apache/doris/qe/SessionVariablesTest.java
@@ -30,6 +30,7 @@
 import org.apache.doris.common.util.ProfileManager;
 import org.apache.doris.common.util.RuntimeProfile;
 import org.apache.doris.load.ExportJob;
+import org.apache.doris.nereids.parser.NereidsParser;
 import org.apache.doris.task.ExportExportingTask;
 import org.apache.doris.thrift.TQueryOptions;
 import org.apache.doris.utframe.TestWithFeService;
@@ -229,4 +230,11 @@ public void testDisableProfile() {
         }
 
     }
+
+    @Test
+    public void testSetVarInHint() {
+        String sql = "insert into test_t1 select /*+ set_var(enable_nereids_dml_with_pipeline=false)*/ * from test_t1 where enable_nereids_dml_with_pipeline=true";
+        new NereidsParser().parseSQL(sql);
+        Assertions.assertEquals(false, connectContext.getSessionVariable().enableNereidsDmlWithPipeline);
+    }
 }
diff --git a/regression-test/suites/nereids_syntax_p0/system_var.groovy b/regression-test/suites/nereids_syntax_p0/system_var.groovy
index 3a3714e8c8161c..42f19ef530aca3 100644
--- a/regression-test/suites/nereids_syntax_p0/system_var.groovy
+++ b/regression-test/suites/nereids_syntax_p0/system_var.groovy
@@ -38,7 +38,7 @@ suite("nereids_sys_var") {
     // set an invalid parameter, and throw an exception
     test {
         sql "select /*+SET_VAR(runtime_filter_type=10000)*/ * from supplier limit 10"
-        exception "Unexpected exception: Can not set session variable"
+        exception "errCode"
     }
 
     sql "select @@session.time_zone"