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Time synchronization is one of core technologies in distributed systems and communication fields. The "Network Time Protocol" (NTP) is the current widely accepted standard for synchronizing clocks over the Internet. NTP uses a hierarchical scheme in order to synchronize the clocks in the network. It mainly adopts a phase-locked loop technique to adjust the local clock. This paper develops a time synchronization algorithm based on frequency adjustment in distributed system, which has a better performance compared with current algorithm, which uses the method of phase adjusting time. Under the same accuracy requirement, the algorithm has much less time requests to the NTP server and higher stability in performance, which decreases a lot on the load of server. This algorithm is more effective and would have preferable value in application.