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Time synchronization is critical in distributed network system. A variety of network protocols, middleware and business applications rely on proper time synchronization across the computational infrastructure and depend on the clock accuracy. The “Network Time Protocol” (NTP) is the current widely accepted standard for synchronizing clocks over the Internet. In order to reduce access frequency to the NTP time server, and efficiently decreases over-loaded phenomena of server. more exactly errors was conclude by adopting Allan variance to analysis the resource, types and statistical characteristics of error which come from clock, measurement and network, and then based on the NTP research and current synchronization algorithm, a new time synchronization algorithm is proposed which is on the basis of a method of combination of adjusted frequency and adjusted phase to attain synchronization between the client with the time server to satisfy more and more accuracy requirement in distributed system applications. Under the same accuracy requirement, the result of the text shows the algorithm is more effective compared with current algorithm, which use the method of phase adjusting time.