The satellite second clock signal is usually used for synchronization in the two-terminal traveling wave positioning device. To eliminate the influence of ionosphere and tropospheric delay, receiver clock error and satellite clock error, a method of generating high precision synchronous clock based on frequency difference regression-difference observation common-view timing model is proposed. Firstly, the frequency difference quadratic regression equation model of crystal oscillator second clock and satellite second clock is established, and the current estimation of regression coefficient of regression equation model is calculated in real time, and the correction value of crystal oscillator second clock is calculated by estimation. The satellite timing differential network is established by using the differential observation common-view timing model to reduce the random drift error of the user’s satellite second clock signal in the transmission process. The modified satellite second clock signal is used as a parameter to improve the fitting accuracy of the frequency difference regression model between the crystal oscillator second clock and the satellite second clock.