The triple modular redundancy design is a common design method for high reliability systems. In the system, mutually redundant modules collaborate through majority voting to complete critical decision control of the system. In order to achieve majority voting and avoid voting errors, mutually redundant modules need to ensure synchronous output of decision results, which requires good synchronization between the three modules. The good synchronization performance ensures that the triple modular redundancy system achieves the reliability expected by the design, and reduces the risk of system error. In the paper, a software based synchronization design method for the triple modular redundancy system can achieve microsecond level inter module synchronization accuracy and meet the synchronization needs of general the triple modular redundancy system.