A autonomous navigation system of a navigational satellite based on X radial pulse satellite includes: an X radial detector, an atomic clock group on the satellite, a planet of our solar system parameter database, an X radial pulsar module and a characteristic parameter database, a computer on the satellite, a strap-down inertial navigation system SINS and an autonomous navigation algorithm module library; in the autonomous navigation method, the X radial photons radiated from the pulsar are used as the input of the external information; the pulse arrival time TOA and the angular position information are obtained; data is processed through a autonomous navigation filter; and the navigational parameters such as the position, the speed, the time and the pose of the navigational satellite; the navigational telegraph text and the control command are generated independently, and the independent running of the navigational satellite is realized. The present invention has the advantages of providing a long time and a high degree of accuracy autonomous navigation, and providing the fault-tolerance capacity of the autonomous navigation information processing. The autonomous navigation system is also be adequate for the high degree of accuracy autonomous navigation of the near earth orbit, the deep space, the interplanetary flight space vehicle, the a celestial body lander without thickset atmosphere and the surface peripatetic machine.