The size of organic matter (OM) pore in shale directly affects shale gas content, and its connectivity is of great significance for gas migration and exploitation. Three-dimension reconstructions down to nanometer scale (about 10 nm) are performed on OM pores in samples from the Lower Silurian Longmaxi Formation in Qiliao area using Focused Ion Beam-Scanning Electron Microscope (FIB-SEM). The results indicate that FIB-SEM technique is an effective method for three-dimension characterization of nano-scale (>3 nm) pore structures of micro-scale shale samples. Honeycomb OM pores distribute uniformly with poor connectivity, and their diameters are dominated by 10-200 nm. Micro-crack like OM pores at the interface exhibit good connectivity on the local area, with diameters concentrated at 200-300 nm. Bulk porosity of shale is positively correlated to OM content. For shale with OM pores as host, the concentrated distribution of the organic matter and the good continuity will result in a small size of unit cell for characterization of porosity.