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 tolerant is achieved by changing software strategy, and no extra hardware is needed to add. The detailed analysis of the proposed strategy is given. Finally, the effectiveness of control strategy is verified.