The invention relates to a multi-clock synchronization method of a distributed type sampling value network, which is applied to a protecting and measuring/controlling system comprising a sampling unit, merging units and a function unit. The method is applied to three scenes: (1) when the sampling unit, the merging units and the function unit are in connection networking and no global time injection exists, establishing time rhythm systems in the merging units, releasing time to the sampling unit and controlling the function unit; (2) when the sampling unit, the merging units and the function unit are in connection networking and global time injection exists, releasing time to the sampling unit or controlling the function unit by the merging units according to global time injection signals; and (3) when the sampling unit, the merging units and the function unit are in connection networking and the global time injection fails, generating main time by a specific merging unit and receiving signals of the main time by other merging units. According to the multi-clock synchronization method disclosed by the invention, needed time synchronization of internal data of the protecting and measuring/controlling system is realized without depending on a global time synchronization system, and the automaticity and the timeliness are high.