Due to the influence of the space radiation environment, the satellite communication system with on-board digital processing capability is prone to single-event upset and seriously affects system reliability. The traditional Fast Fourier Transform(FFT) scheme based on the remainder check has a large number of butterfly operations, and the rotation factor needs to be expanded by a certain multiple to ensure accurate calculation, resulting in greatly increased complexity. In order to solve this problem, the data is cut off in the middle stage of the FFT, and a single sampling decision module is added before truncation to ensure correct data output. At the same time, a new simplification is proposed for the modulus operation added in the above process. Through functional simulation and comprehensive proof, the proposed scheme achieves an effective reduction of hardware resource occupation overhead.