To reduce the mismatching and non-matching in the protein two-dimension electrophoresis (2-DE) images, we proposed an auto-matching algorithm based on gray hierarchical and geometric blocking in this study. Firstly, protein spots in the gel images were divided into groups by gray level and geometric position, and then a method based on shape context and normalized correlation was used for coarse matching in protein spots. Secondly, matched pairs in coarse matching were set as feature points, and the precise matching in the rest of not matched protein spots was accomplished by the method of geometric correlation and similarity criterion. Finally, local affine transformation was used in the verification of matching results to remove non-matching and mis-matching points. The algorithm was applied to different 2-DE gel images. The results showed that the new matching algorithm could reduce the non-matching and mis-matching spots, and increase the matching accuracy.