The measurement and control system of the satellite contains ground-based tracking system and space-based tracking system. The ground-based tracking system contains united S-band (USB) system and laser tracking system etc. At present the space measurement and control system of our country mainly bases on ground-based tracking system. At which several shortages emerge with the improvement of the requirement of the space measurement and control system and the development of the navigation system of our country, satellite-based navigation system becomes more and more important in measurement and control system. With the foundation of COMPASS navigation system, it's urgent to research the strategy of orbit determination based on satellite-based navigation system. New theory was brought forward, based on the theory of satellite-based navigation system. Firstly an algorithm of visibility and inter-satellite measurement model was presented, visibility and position dilution of precision (PDOP) were analyzed, following the dynamic characteristic was analyzed considering the reserving capacity of the receiver, lastly extend kalman filter(EKF) was used for realizing HEO autonomous orbit determination. The simulation results indicated that the number of the visible navigation satellite reached to 0 similar to 3, little to 4, when its orbit altitude was higher than navigation satellite, PDOP reached to 1 similar to 6, the position precision could reach to magnitude of lm,the velocity precision reached to magnitude of one millimeter per second, which indicated this method could be used for HEO autonomous orbit determination.