Analysis of the three-dimensional (3D) visualization and reconstruction methods of nanopores, and its morphology and connectivity are the key to explore the storage and migration mechanism of coalbed methane (CBM). The Bofang (BF) sample collected from the Qinshui basin was scanned by the focused ion beam scanning electron microscopy (FIB-SEM), which can simultaneously image the nanopores through 2D slice image and 3D reconstruction image. Firstly, the 2D morphology and development characteristics of nanopores were analyzed. Secondly, the 3D visualization and reconstruction of nanopores were carried out. Then, the pore connectivity, permeability, and geometric characteristics were discussed. Finally, the effect of pore structure on the storage and migration of CBM was emphatically analyzed. The results show that the organic pores, inorganic pores, shrinkage-induced pores and micro-fractures were developed in coal, and their morphology and connectivity were significant differences. The pores and throats can be extracted from the digital cores with sub-volume of 4.9 × 4.9 × 4.5 μm3, the pore number and throat length (avg.) of BF sample are 21951 and 18.2789 nm, respectively, the porosity and permeability of BF sample is 2.004% and 4.405 × 10−3 mD, respectively, which all indicates the BF reservoir has good storage and connectivity capacity. For pores <50 nm, the number, volume and area indicate that the BF sample has good storage capacity. For pores >200 nm, the pores are all interconnected, which indicates the BF sample can provide effective channels for CBM migration. The distribution of pores and throats and their geometric and topological structures indicate that the BF sample has good migration ability. This study on the methodology of 3D visualization and quantitative characterization of nanopores using FIB-SEM can broaden the research method of pores, and lay good foundations for studying the storage and migration of CBM.