Aiming at the problem that the time on the satellite deviates from the time of the entire network constellation caused by the abnormal jump of the satellite clock, an autonomous time synchronization algorithm for Beidou-3 satellites for the jump of the satellite clock is designed. By introducing robust least-squares estimation, the time synchronization algorithm of distributed satellite constellations was improved, so that it can quickly detect abnormal clock jumps and have the ability of autonomous time synchronization. Using the same simulation environment as the Beidou-3 satellite and introducing actual on-orbit test data, the algorithm was accurately evaluated. The results show that within 60 d, the time synchronization error of each satellite in the constellation does not exceed 368 ns, and when a satellite jumps abnormally, the algorithm can restore time synchronization within 1 h, which improves the reliability of the algorithm under clock jumps.