Abstract: In order to ensure the navigation accuracy of long time navigation systemand and improve the ability of clock error control, X-ray pulsar and Doppler difference integrated navigation method for correction of clock difference is proposed.X-ray pulsar navigation is measured by pulse arrival time, Doppler differential navigation utilizes the difference between the two moment Doppler velocities relative to the sun. The difference between the two Doppler velocities not including Doppler speed deviation can be used as navigation measurement information. The onboard clock error is augmented into the new state variable, the integrated navigation system is established, and the federated unscented Kalman filter(UKF) is used to fuse the navigation information.The simulation results show that the method can suppress the influence of Doppler velocity deviation on navigation, control the clock difference on the onboard clock, and provide higher navigation estimation accuracy.