Abstract: SEM(Soft Error Mitigation)IP is an effective method of single event fault injection for SRAM FPGA design. However, the target design and the SEM IP part are randomly placed and routed on the same chip, when fault injection is performed, the configuration register used by the SEM IP is likely to be overturned, causing the fault injection system to stop working and the failure rate of the target design is not accurate. To solve this problem, a single event fault injection prototype system based on SEM IP and partial reconfiguration technology is developed for single particle injection. The method places and routes the SEM IP and the target design to different areas of the chip, can only perform fault injection into the area where the target design is located without interrupting SEM IP operation itself. Besides, the area of the target design can be reconfigured when an uncorrectable error occurs. The method needs less configuration data and shorter time, which greatly improves the efficiency of fault injection experiment and the accuracy of the target design soft failure rate estimation.