The traditional redundancy fault handling method would lead to the safety degradation of flight control computer system in the case of local faults. When the residual redundancy problems occur again, the flight safety and the completion of the mission will be endangered. The reliability of flight control computer can be effectively improved by fault redundancy restart and recovery synchronization. By analyzing the redundancy synchronization process of system power-on and restart, the single-channel fault restart synchronization process and dual-channel restart synchronization process are studied, so as to improve the reliability of the flight control system and ensure the quality of the flight control system.