The distribution line possesses many branch lines and complex topological structure, so applying the traditional differential protection to distribution line will cause big investment cost and complex management. The distribution automation system based on EPON will overcome these shortcomings by using EPON channel to realize the multi-terminal differential protection, but the sampling value synchronization is a difficult point. Aiming at communication features of EPON, this paper introduces a clock synchronization protocol similar to IEEE 1588. It simplifies the interaction mechanism of IEEE 1588 master-slave clock, and realizes the clock synchronization between the main device and slaves. The accuracy can meet the demand of distribution line multi-terminal differential protection. Tests show the proposed method can solve the problem of clock synchronization under the EPON communication.