Abstract: The method of autonomous navigation based on X-ray pulsars is steady, credible and with high- accuracy. It is an important approach in the spacecraft navigation field. In this paper, firstly, the algorithms of autonomous navigation based on X-Ray pulsars are introduced; secondly the model of the extended Kalman filter which is used in the autonomous navigation based on X-Ray pulsars is established; thirdly, taking the geosynchronous orbit for example, the accuracy of navigation with different initial error, different incline of orbit, different eccentricity of orbit and different orientation error of the pulsars are simulated. With 0.001 second accuracy of pulsar orientation and 0.1 accuracy of the time of pulse arrival, from the results, it can be seen that the position accuracy of the geosynchronous orbit can reach 1\,km, and the accuracy of navigation is immune with initial error. It is also shown that the orientation of pulsars, the accuracy of the time of pulse arrival, the position of the orbit plane and the eccentricity of orbit are the main factors which influent the accuracy of navigation.