Abstract: The Pulse Per Second(PPS) signal of Global Positioning System(GPS) receiver has large random error and the onboard clock exists cumulative error. Based on analyzing normal distribution characteristics of the PPS signal of GPS, the real-time correction algorithms for reference source of PPS and clock were proposed. In the real-time correction algorithms for reference source of PPS, the average value of pulse number in one second was obtained by averaging high frequency pulse accumulation, the average value of time error was obtained by averaging the pulse number of the time error between predict second pulse and coordinated universal time(UTC), thereby generating corrected second pulse. On the basis of the actual frequency of Temperature Compensated Crastal Oscillato(TCXO) which is obtained by the average method, pulse compensation algorithm was studied which is used for correcting the clock reference source. Simulation and experiment results show that the random error decreases 7.5 times by the use of real-time correction algorithm for reference source of PPS. Test error is less than 140 ns in 9.5 hours by the use of real-time correction algorithm for reference source of clock. The real-time correction algorithm for reference source can effectively reduce the errors based on PPS signal of GPS.