By introducing the requirements of time synchronization（TS）， the technical characteristics， operation principle and the networking methods of network time protocol in smart substations， the advantages and shortages of the network TS system are analyzed. To solve the potential security risks of system management， product design and network architecture caused by IEC 61588 network TS system， a security evaluation method based on the simulation technique under network traffic for smart substation is proposed. The proposed method has been used to analyze a case， and the safe and reliable operation of the IEC 61588 TS system is ensured.