Abstract: Power supply prototype in High Intensity heavy ion Accelerator Facility-Booster Ring (HIAF-BRing) adopts the scheme of full energy and fast cycle storage pulse power supply topology. Its multi modules are connected in series and parallel pattern, and the power reaches megawatt level. Due to the high power and large scale of the power supply, a module fault interlock protection system based on Programmable Logic Controller (PLC), interlock boards and Field Programmable Gate Array (FPGA) is designed and implemented to protect the power supply in operation. In this paper, first, a design of double redundant module fault interlock is introduced. Second, the logic implemented in PLC is described. Third, the work about FPGA is given. Finally, the system is tested in three aspects: the responsive time of the power supply interlock loop, the total time from controller error occurrence to interlock finish, and the equipment fault response. The result shows that the module fault interlock system can action sensitively, timely and reliably in case of fault occurrence, which meets the requirements of the power supply prototype in HIAF-BRing.