The difference between equipment on-orbit and equipment on-earth is that the manufacturing cost is high， and the adaptability requirements for the space environment are high. In order to extend the life of the spacecraft and improve the reliability of the on-orbit equipment， it is necessary to consider the maintainability needs of the spacecraft.Aiming at the requirements of on-orbit software and functional maintenance of space systems， this paper focuses on space highly reliable on-orbit reconfiguration technology under the background of space environment application. Based on the extensiveness， flexibility and reliability of FPGA in spacecraft applications， a highly reliable on-orbit reconfiguration system based on FPGA architecture is designed. The advantage of the architecture is that it makes full use of the hardware architecture of "SRAM FPGA+antifuse FPGA" commonly used in equipment on-orbit， and only adds the on-orbit reconfigurable function through software changes on the basis of realizing the SRAM FPGA dynamic refresh function， which greatly reduces the cost of hardware change and expands the application of reconfigurable function.This paper gives a specific scheme of one spacecraft project， which verifies the feasibility， scalability and reliability.