The research object of core analysis is a system consisting of complex pore geometry, rock matrix and multi-phase filling. But in the traditional core experiment, the micro pore structure of core can't be directly observed or controlled. With image processing technology, CT image is enhanced and it highlights more useful information. Core image are basically binary processed in the core area. This article introduces a multi-level thresholding segmentation method based on Otsu, through which, the core image are three-valued changed. Compared to the binary image, three values images provide researchers more information. Based on those images, marching cubes algorithm is used to reconstruct digital core. This digital core resembles real rock and it can show some true information of the reservoir. It also has the important meaning to the core research.