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In order to promote the practical application of clock synchronization in distributed simulation system, the specific requirements of clock synchronization system are identified. After comparing various clock synchronization schemes, NTP scheme is selected and optimized. On the basis of introducing the basic principle of NTP clock synchronization, this paper analyzes the influence factors of clock synchronization accuracy, creatively puts forward three optimization methods: constructing high-precision logic clock, optimizing the asymmetry of network loop round-trip delay by inequality method, and on-line compensation of clock crystal frequency, and establishes the clock synchronization system. The experimental results show that the synchronization accuracy of the designed clock synchronization system is better than 1ms, and the average calibration period is about 5h. The clock synchronization system can be encapsulated as a DLL, which can be flexibly integrated into specific projects.