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Time synchronization of Substation Automation System (SAS) based on IEC61850 is studied in this paper. According to the request of time synchronization in SAS, the Network Time Protocol (NTP) is applied to SAS. Following the idea that the time offset is essentially caused by the frequency of clock itself so that it can be used for time synchronization with little or no additional cost, a new algorithm is presented, which adopts statistical technique to adjust the system clock frequency. The experimental results show that our algorithm has good performance to reduce the access frequency of time server and smooth time curves as well as meet the requirement of time synchronization in substation level.