Aiming at the long time in-orbit navigation of spacecraft, a fully autonomous navigation system based on SINS/Ultraviolet sensor/Star sensor is proposed. With the Ultraviolet sensor for positioning and the Star sensor for attitude determination, a higher navigation precision can be reached. Then the state model and the measurement model for this integrated navigation system are constructed in the inertial frame. The spacecraft attitude is represented by the MRPs in these models, for large initial misalignment angle or large angle maneuver as orbit transfer. At last, the EKF and UKF filter method are used for both low orbit and high orbit spacecraft. The simulation results show that the positioning accuracy is as high as 310m even for geosynchronous orbit spacecraft.