In order to improve the reliability of CubeSat’s reconfigurable OBC (On Board Computer) with minimum cost, a reconfigurable CubeSat on board processing system with FPGA (Field Programmable Gate Array) is proposed. First, according to the analysis of OBC design character in micro/nano satellite at home and abroad, FPGA based on the SRAM (Static Random Access Memory) architecture and Flash architecture are both adopted as the core process module and external vote interface module, respectively. By doing this, the system operation speed and reliability are both considered simultaneously. Second, the reconfigurable strategy, the online reconfiguration technology and the synchronization technology are discussed in detail. Finally, the tests on the designed hardware system and the operation data in orbit both verify the reliability and effectiveness of the designed architecture.