Aiming at the multi-frame short exposure image overlay, this paper proposes a method that integrates the angle information of the imaging system and obtains the image offset pixels through the coordinate transformation calculation between the optical system and the camera system. For the angle of each frame of a short-exposure image, the geometric relationship of the optical system is used to perform sub-pixel offset registration, and the Fourier spectral filter H(u, v) is constructed through the frequency shift characteristic of the Fourier transform. The image is corrected at the sub-pixel level in the frequency domain, and the high-frequency response of the image is evaluated by the edge method. Compared with that of the unrepaired image, the line pair of the image corrected by the proposed algorithm is increased from 20 lp/mm to 33 lp/mm at a modulation transfer function (MTF) attenuation of 50% (MTF₅₀), with its repair effect higher than that of the traditional quadratic interpolation algorithm. The proposed algorithm shows a positive repair effect in the line pair part of 40-80 lp/mm, and the peak value of the MTF is increased by four times.