Abstract: To improve the stability and accuracy of precise time protocol (PTP) master clock source in smart substation, the traditional calibration method of PTP master clock source usually uses the Pulse Per Second (PPS) clock difference signal output by GPS and PTP master clock to generate crystal frequency adjustment signal, according to which the PTP master clock source is calibrated. The traditional clock difference signal processing does not take into account the jump outfield of PPS, the nonlinear error caused by the crystal temperature change, and the crystal aging of the master clock source. To solve the above problems, this paper firstly conducts mathematical modeling for PPS clock difference signal output by PTP master clock and GPS and then conducts filtering processing for PPS clock difference signal based on new information sequence weighting and adaptive Unscented Kalman Particle Filter (UPF) algorithm. Finally, the crystal frequency adjustment signal is generated from the processed clock difference signal by the PID controller to realize the calibration of the PTP master clock source. The UPF technology is used to correct the master clock source frequency nonlinear drift due to aging, introduce new information sequence weighting technology can process jump outliers of the GPS second pulse signal, adaptive filtering technique can reduce the noise influence on filtering result, enhance the clock source calibration system robustness, and improve frequency precision. Simulation results show that compared with the traditional clock offset signal processing algorithm, the algorithm in this paper reduces the clock offset signal processing error by 55.96%, and the clock offset processing error at the jump outfield value by more than 76%, thus reducing the intermediate frequency offset measurement error of the PTP master clock source calibration system from 3.635×10^–10 to 9.59×10^–12. Finally, the frequency stability of the PTP master clock source is improved by two orders of magnitude.