To overcome the large size and poor portability of MCP-PMT traditional high-voltage power supply equipment, a high-voltage power supply mode based on miniaturized high-voltage module is adopted. During the practical use of the system, a high-voltage breakdown fault of MCP-PMT occurred. In this paper, the fault causes of the system are analyzed in detail, and the problem is identified as the decline of withstand voltage performance caused by the decline of internal vacuum of MCP-PMT, and it is also found that the high voltage overshoot of the high voltage module at the time of power-up is the cause of this fault. Aiming at the overshoot problem of high-voltage module, this paper puts forward a more ingenious design improvement method and achieves good results, which further improves the engineering application reliability of MCP-PMT system.