The high-voltage and high-power spacecraft power system is the developing trend for the requirement of the future space exploration tasks. Due to the effects of space radiation, the selection of the high-voltage power device is limited in spacecraft power system application. Thus, the multi-level power converter is a good solution for the high-voltage and high-power spacecraft power system. In this paper, the fault-tolerant strategy of three-level flying capacitor DC/DC converter is proposed to increase the reliability of the converter. The fault tolerance is achieved by changing software strategy, and no extra hardware is needed to add. The fault-tolerant strategy for three-level flying capacitor converter is proposed in this paper. It improves the reliability of the three-level DC/DC converter. First, the control scheme is introduced. Second, the analysis of the converter under fault tolerance is given. Finally, the proposed strategy under different conditions is verified.