In this paper, the solution to dislocation between adjacent rows is proposed for the advanced geosynchronous radiation imager (AGRI) of Fengyun-4A (FY-4A). Firstly, according to the scanning mode of AGRI combined with the shift theorem of the Fourier Transform, the phase difference curve of adjacent pixels in the misaligned row is calculated. Secondly, the displacement value is obtained by fitting the low frequency portion of the phase difference spectrum by the least squares method. Finally, the dislocation rows are reconstructed by means of “weight assignment” according to the displacement value, and the problem of dislocation between the rows is solved. The scheme proposed is verified by simulation experiment, and the in-orbit images of AGRI are processed. The results show that the proposed algorithm can achieve registration between adjacent rows with high precision on sub-pixel level.