Abstract: Aerospace and extra-terrestrial applications on SRAM FPGA are sensitive to SEU which might result in information loss or functional interruption. In this paper, a detailed introduction to TMR and Scrubbing, which are the significant techniques of this design, was given; then, a highly reliable fault-tolerant system based on TMR, Scrubbing and Reload rules was implemented. An anti-fuse FPGA periodically scrubbed the configuration bitstream of SRAM FPGA in milliseconds level, and both FPGAs implemented triple module design redundancy. This fault-olerant design has been adopted in an actual spacecraft electronic system, which can make reference to the design of highly reliable electronic systems.