Abstract: The clay rock in coal stratum is scanned non-destructively by micro-CT, and the algorithm of rock pore structure (the porosity and the pore aperture) is studied by use of Matlab based on the micro-CT image. The results show that the combination of micro-CT scanning, digital image processing and three-dimensional reconstruction can provide a new, simple and feasible method for the analysis of rock pore structure. The computer system of micro-CT experiment can generate CT single section and the porosity of rock is calculated by use of digital image processing. The new images with different resolutions are generated by image compression. When the pixel sizes of the new images are taken as the pore aperture, the rules of the rock porosity variation with the pore aperture are estimated on micro-CT single image. The volume rendering algorithm of visualized reconstruction can make the sequences which stem from the single image generate three-dimensional digital image, by which the rock porosity and the pore aperture are computed. For example, with the increase of the pore aperture, the porosity of clay rock in coal stratum is reduced by the negative exponent rule, and the result is identical with the aperture distribution measured by mercury porosimeter method.