For deal with the problem of rectification of mismatching pairs in 2D images that are taken in the process of spacecraft’s autonomous optical navigation, a method of sample consensus based on combination and sorting (SACCS) is proposed for affine transformation matrix estimation. In this paper, theory of SACCS is firstly introduced and followed by an example, and then, rectification of mismatching pairs is proposed based on SACCS. Finally, a serious of comparison with RANSAC is conducted to test the performance of SACCS.