In the time synchronization of regional navigation systems, the outlier of the time difference caused by the measurement data jump due to the influence of dynamic, interference and measurement information that cannot be shared in time will decrease the accuracy of time synchronization and seriously affect the performance of time synchronization of regional navigation systems. In the paper, a time synchronization contention method between regional navigation stations is presented based on the bidirectional time comparison synchronization technique, and a time synchronization outlaw elimination method and filtering method between stations are proposed to solve the problem of time difference measurement value caused by uncertain factors and improve the performance of time synchronization between stations. The feasibility of the method is verified by the implementation of the method in the regional navigation system and the field test.