In the distributed aperture synthesis imaging system based on digital holography, the errors of detector rotation and the pupil magnification among the sub-apertures are studied, and the correction methods based on the sub-aperture image registration is proposed. The scale-invariant feature transform algorithm, the nearest neighbor search method based on Euclidean distance and the M-estimator sample consensus algorithm are carried out to realize the image registration of sub-aperture, so that the errors of relative rotation angle and magnification among the sub-apertures are calculated. Then the complex amplitude of object light is processed to correct the rotation and magnification errors. The experimental results show that the calculated relative error values are less than 0.01, and the sharpness value of synthetic aperture image is significantly improved after correction.