Abstract: The autonomous navigation is the key technology to realize the interplanetary exploration,the principle of navigation based on X-ray pulsars is steady,credible and high-precision which is free from the limits of the near earth space and provides a new thought to the autonomous navigation.The navigation principle based on the X-ray pulsars was studied,the algorithm of predicting TOA and the method of solving the ambiguity points were put forward,and the method of estimating the position based on the Least Square theory was studied.The results show that,with 0.001 arcsec accuracy of pulsar direction and 1μs accuracy of the time of pulse arrival,the position accuracy can reach 10km during the 140 days' flight and the navigation accuracy is not sensitive to the initial error,autonomous navigation based on X-ray pulsars can satisfy the requirements of interplanetary exploration.