Among the technologies of intelligent substation, the accuracy of time synchronization plays an important role in the information collecting, fault analyzing, detection controlling. The IEEE 1588 time synchronization protocol enables the accuracy of microsecond, which becomes the ideal choice to realize the accurate network time synchronization of substation. In this paper, the realization mechanism of IEEE 1588 protocol was introduced first, and on that basis, the main accuracy influencing factors of the protocol were analyzed. Aiming at the influencing factors, the specific methods to improve the synchronization accuracy were proposed. The research results could provide theory references for the accuracy improving of IEEE 1588 time synchronization protocol.