diff --git a/tests/scripts/thread-cert/Cert_5_3_03_AddressQuery.py b/tests/scripts/thread-cert/Cert_5_3_03_AddressQuery.py
index 36c37ba42..5ae571a5d 100755
--- a/tests/scripts/thread-cert/Cert_5_3_03_AddressQuery.py
+++ b/tests/scripts/thread-cert/Cert_5_3_03_AddressQuery.py
@@ -108,9 +108,12 @@ class Cert_5_3_3_AddressQuery(unittest.TestCase):
         self.assertEqual(self.nodes[DUT_ROUTER2].get_state(), 'router')
         self.assertEqual(self.nodes[ROUTER3].get_state(), 'router')
         self.assertEqual(self.nodes[MED1].get_state(), 'child')
-        dut_messages = self.sniffer.get_messages_sent_by(DUT_ROUTER2)
+
 
         # 2
+        # Flush the message queue to avoid possible impact on follow-up verification.
+        dut_messages = self.sniffer.get_messages_sent_by(DUT_ROUTER2)
+
         router3_mleid = self.nodes[ROUTER3].get_ip6_address(config.ADDRESS_TYPE.ML_EID)
         self.assertTrue(self.nodes[MED1].ping(router3_mleid))
 
@@ -120,6 +123,12 @@ class Cert_5_3_3_AddressQuery(unittest.TestCase):
         command.check_address_query(msg, self.nodes[DUT_ROUTER2], config.REALM_LOCAL_ALL_ROUTERS_ADDRESS)
 
         # 3
+        # Wait the finish of address resolution traffic triggerred by previous ping.
+        time.sleep(5)
+
+        # Flush the message queue to avoid possible impact on follow-up verification.
+        dut_messages = self.sniffer.get_messages_sent_by(DUT_ROUTER2)
+
         med1_mleid = self.nodes[MED1].get_ip6_address(config.ADDRESS_TYPE.ML_EID)
         self.assertTrue(self.nodes[ROUTER1].ping(med1_mleid))
 
@@ -129,7 +138,12 @@ class Cert_5_3_3_AddressQuery(unittest.TestCase):
         command.check_address_notification(msg, self.nodes[DUT_ROUTER2], self.nodes[ROUTER1])
 
         # 4
+        # Wait the finish of address resolution traffic triggerred by previous ping.
+        time.sleep(5)
+
+        # Flush the message queue to avoid possible impact on follow-up verification.
         dut_messages = self.sniffer.get_messages_sent_by(DUT_ROUTER2)
+
         self.assertTrue(self.nodes[MED1].ping(router3_mleid))
 
         # Verify DUT_ROUTER2 didn't send an Address Query Request.
@@ -138,12 +152,15 @@ class Cert_5_3_3_AddressQuery(unittest.TestCase):
         assert msg is None, "The Address Query Request is not expected."
 
         # 5
-        dut_messages = self.sniffer.get_messages_sent_by(DUT_ROUTER2)
         self.nodes[ROUTER3].stop()
 
         # Wait for the Leader to expire its Router ID.
         # MAX_NEIGHBOR_AGE + INFINITE_COST_TIMEOUT + ID_REUSE_DELAY + propagation time + transmission time ~ 580s.
         time.sleep(580)
+
+        # Flush the message queue to avoid possible impact on follow-up verification.
+        dut_messages = self.sniffer.get_messages_sent_by(DUT_ROUTER2)
+
         self.assertFalse(self.nodes[MED1].ping(router3_mleid))
 
         # Verify DUT_ROUTER2 sent an Address Query Request to the Realm local address.
@@ -154,6 +171,10 @@ class Cert_5_3_3_AddressQuery(unittest.TestCase):
         # 6
         self.nodes[MED1].stop()
         time.sleep(MED1_TIMEOUT)
+
+        # Flush the message queue to avoid possible impact on follow-up verification.
+        dut_messages = self.sniffer.get_messages_sent_by(DUT_ROUTER2)
+
         self.assertFalse(self.nodes[ROUTER1].ping(med1_mleid))
         self.assertFalse(self.nodes[ROUTER1].ping(med1_mleid))