The physiological and pathological changes of organisms will have certain effects on the morphology of tissues and organs. Conversely, the morphological changes of tissues and organs can also reflect the physiological and pathological changes of organisms to some extent. The bio-tissue slice can provide people with two-dimensional information of the tissue structure on a certain section. In this paper, the image registration algorithm based on mutual information is used to register the slice images of different tissues, and then the image segmentation is used to improve the registration accuracy. The three-dimensional data of the organizational structure is obtained, and the three-dimensional image of the tissue is reconstructed by computer processing. The reconstruction of different tissue slices is used to prove that the algorithm is fast and accurate, and the reconstruction speed of the 3D model is improved, which is of great significance for shortening the diagnostic waiting time.