Abstract: Three dimensional (3D) structures of nanometer scale pores is a determining factor for the shale gas micro-seepage mechanism, and it is a critical issue needing to be solved urgently to develop a better model for the description of flow behavior in shale. In this study, 3D structure of the OM pores of the Longmaxi formation shale sample (Φ=7 μm) from the Sichuan basin was rebuilt using synchrontron radiation CT and experimental CT respectively. The purpose of the study was to compare the pore structural parameters obtained from the radiation CT and experimental CT. The results indicate:(1) The OM pores, with a porosity of about 60%, exhibit a honeycomb pattern and good connectivity. The pore size distribution exhibits a bimodal pattern, mainly concentrating in 60-150 nm and 500-1400 nm, and pores with diameters larger than 500 nm contribute the most to the total porosity. (2) The porosity and the total pore number obtained from synchrontron radiation CT and experimental CT remain consistent within the accepted margin of error, but the total throat number and throat diameters obtained from the second method above suggest a relatively large difference. Although the pore size distribution and coordination number distribution laws are similar, there are obvious deviations considering the exact figures. (3) For 3D characterization of shale pore structures using nanometer CT, there are problems of threshold partition and small scan view. The problems can be reduced by three plans starting with reconstruction algorithm, 3D data analysis and REV.