With the development of digital and intelligent trend of substation, higher requirements on communication network were put forward. With features of high bandwidth, low cost, high reliability, easy maintenance, EPON has been widely applied in the field of distribution communication network. But precision of time synchronization is insufficient while bearing intelligent substation services by EPON. For providing sub microsecond time synchronization, IEEE 1588v2 can solve this problem. Based on depth study of EPON synchronization technology and IEEE 1588v2 protocol, a novel method to implement high-precision time synchronization based on EPON technology in intelligent substation is proposed. Through test, the proposed scheme has very good time synchronization performance. It can well meet requirements on precise time synchronization in intelligent substation.