This paper designs a kind of on-board FPGA reconfigurable method, improves configuration reliability of onboard signal processing FPGA by making use of hardware three-mode redundancy and software three-mode comparison. By sending the erase, write and read instructions to the satellite configuration FPGA, the erase, program and read for the onboard data storage FLASH are realized, so as to realize the reconfiguration of the onboard signal processing FPGA, and then realize the on-orbit update or upgrade of the payload function, reduce the repetitive development of hardware and the cost.