Abstract: Measurement based on X-Ray Pulsars is not only able to provide stable and reliable position, velocity and attitude information for deep space probe, but also can correct the long term bias of the atomic clock in the probe. Especially for the Mars exploring missions, the flight time of Mars probe is fairly long so that the clock bias is accumulating continuously, which will greatly damage the accuracy of the Mars probe autonomous positioning and timing system. In this paper, a novel synchronous Positioning/Timing method for Mars probe is proposed based on the principle of synchronous positioning and timing by X-Ray pulsars. And the clock correction is modeled accordingly. Pulsar optimization factor is used to conduct the optimal selection of pulsars. Then the Positioning/Timing model is presented and the clock corrections based on the new clock model are estimated together with the position and velocity of the Mars probe by using the adaptive extended Kalman filter. So that the position, velocity and clock model parameters of Mars probe could be calculated synchronously. Simulation experiments are carried out based on the proposed method. Results show that the clock bias can maintain in 300ns, while the position and velocity accuracy of Mars probe is better than 200m and 0.03m/s after corrected, respectively. Conclusions could be drawn that the proposed method of Mars Probe Autonomous Positioning and Timing Based on X-Ray Pulsars could overcome the initial state error effectively and obtain more accurate filter value of position, velocity and clock parameters for Mars probe.