Under GNSS autonomous navigation mode, in order to keep constellation stabilization and integrity, failure satellites must be separated in time. A GNSS autonomous navigation integrity separation technique was developed, and satellite failure judgment method was analyzed. Satellite failure separation procedures were designed, and then a failure check and separation technique was presented. Simulation of this technique suggests that it ensures services precision by effectively separating failure satellites among autonomous navigation constellation. Furthermore, this technique is not very complex and easy for engineering.