Time synchronization is a prerequisite in sensor network applications such as object tracking, consistent state updates, duplicate detection, and temporal order delivery. In addition, reliability issues and fault tolerance in sophisticated sensor networks have become a critical area of research today. However, most research on time synchronization does not consider clock faults of nodes such as fluctuation, severe changes in drift rate, and so on. In this paper, we propose a fault tolerant time synchronization method for wireless sensor networks. In the proposed method, two cases of fault model: (1) clock faults and (2) network faults (topology changes) are assumed. In order to evaluate the performance of the proposed method, a simulation model is established in the NESLsim based on the PARSEC platform. In the simulation, the effect of clock faults is analyzed. Simulation results show that the proposed scheme has about 1.5x~2x better performance than TPSN (Timing-sync Protocol for Sensor Networks) in the presence of faults.