Time synchronization protocol is an important part of wireless sensor networks. Many applications and communication protocols of wireless sensor networks are built on the basis of an accurate synchronized timing. The previous time synchronization protocol for wireless sensor networks focuses on how to improve the accuracy and reduce related energy consumption, but now the security problem of time synchronization protocol in wireless sensor networks is catching people’s attention. This paper designs a new fault-tolerant time synchronization protocol (FTTSP) for wireless sensor networks with random weighting estimation, based on the analysis for the attack to time synchronization protocol for wireless sensor networks. Simulation results show that the protocol has good intrusion detection capability and fault tolerance to malicious synchronization information.