Frequency-domain anti-jamming technology is a common anti-jamming method for satellite navigation receivers. 1/2 overlapping windowing can effectively solve the spectrum leakage in the frequency domain conversion process, but the traditional window function will cause the loss of signal energy. This paper proposes a window function design method with no loss of signal energy, which can effectively solve the signal energy loss caused by the window function. The feasibility of the proposed method is theoretically deduced, and the effectiveness of the proposed method is verified by simulation and measured data. Compared with the traditional window function, the signal-to-noise ratio improvement of the method proposed in this paper is better than 0.5 dB. The frequency domain anti-jamming processing is optimized, the signal-to-noise ratio loss caused by the anti-jamming processing is reduced, and the anti-jamming performance is indirectly improved. This plays an important role in the performance optimization of satellite navigation system links.