In this paper, high reliability radiation hardened On-Board Computer system using reconfigurable FPGA is investigated for space application. To avoid the influence of single event effects caused by an energetic particle in space, a new design scheme of high reliability OBC system is proposed using two FPGA chips and four DSP chips. The overall structure is based on redundant and reconfigurable technologies. The system adopts a 'parallel + backup' structure, the system control unit realized on two FPGA working in dual CPU cold-redundancy mode. The DSP system containing three DSP chips is designed based on triple modular redundancy theory, the rest DSP serves as a backup DSP. Then, complete and reliable faults tolerant methods and reinforcement strategies are realized through software. The proposed design scheme can greatly improve the reliability of OBC system based on in-depth analysis, and has great potential for space applications.