The reliability of the device is very important in the complex space electromagnetic environment where the circuit is greatly affected by cosmic rays and single particles. Anti-fuse Field Programmable Gate Array(FPGA) is a one-time programmable device with anti-fuse as the basic programming structure. Since the state of anti-fuse FPGA cannot be reversed after programming, it has the advantages of non-volatility, high confidentiality, high reliability, and radiation resistance, which is very suitable for aerospace and other fields. A design scheme of anti-radiation wave control unit based on domestic anti-fuse FPGA is presented to solve the problem of radar array in space electromagnetic environment. The domestic anti-fuse FPGA chip is taken as the core in the proposed scheme. The working principle and realization block diagram of the system circuit are given, and relevant experiments are conducted. The experimental results show that the transmission delay of RS422 is less than the symbol period under the baud rate of 5 MHz, and the phase distribution time of the 144-unit phaseshifting component is less than 500 μs, which meets the design requirements.