Abstract: Since it is very difficult for ground mission and control segment to monitor the satellite’s state all time and in the invisible region, a substitute integrity monitoring method depending on inter-satellite-links is proposed. It mainly focuses on designing and simulation for satellite autonomous integrity monitoring based on inter-satellite-links. By separating clock error and ephemeris error based on ISL observation, the algorithm how to detect the anomaly of satellite clock and ephemeris is studied. The method based on balanced time sequence is studied for detecting the clock anomaly, and the method based on non-centric and square distribution is studied to detect the orbit anomaly. Through the simulation and analysis it is shown that the algorithm based on ISL can detect the anomaly of clock and orbit, and the integrity risk of the satellites navigation system is reduced, and the time of alert is shorten, so the integrity performance of GNSS is enhanced.