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In this paper, we proposed a registration algorithm based on the combination of pyramid hierarchical idea and graph theory. It can solve the challenging problem of extracting consistent characteristics and matching the infrared and visible images. First, extracting the maximally stable extremal regions (MSERs) in the determining maximum down-sampling images and each MSER is represented by a polygon. Then constructing the gragh features and the mapping relationship of MSERs between the infrared and visible images are determined by the graph matching method. Next we can construct the initial point set for matching according to the mapping relationship. Finally, using the random sample consensus (RANSAC) algorithm to obtain the optimal parameters and determine the error evaluation parameters. According to the idea of pyramid stratification, the above process is repeated in the high resolution images under the constraint condition of current matching error. The experiment results show that the algorithm can make full use of the visual similarity structures between images, and can achieve a smaller matching error under the premise of ensuring the robustness of the matching.