Abstract: We used a Focused Ion Beam Scanning Electron Microscope (FIB-SEM) to observe the pore structures of the Lower Cambrian Niutitang shale and the Upper Ordovician Wufeng to Lower Silurian Longmaxi shale, sampled in the southeast of Chongqing.Three-dimensional distributions of the nanometer-sized organic-matter pores were reconstructed and their pore structure parameters were analyzed quantitatively. Our work indicated that microfractures between strata, interparticle and intraparticle pores in the mineral matrix, and organic-matter pores were well-developed in the Wufeng-Longmaxi formations. Pores within organic matter form a well-distributed honeycomb like structure with good connectivity, and the pore radius is between 3 and 100 nm. Porosity of organic matter calculated using the FIB-SEM 3-D reconstruction is between 9.13% and 18.42%,and the contribution of organic-matter pores in the total porosity is correlated with the total organic carbon (TOC) content. Dissolution pores and interparticle pores are developed in the Niutitang Formation while organic-matter pores are unevenly distributed. The organic-matter pores are tabular or pinhole with the pore radius between 3 and 25 nm and have poor connectivity. The calculated organic-matter porosity is below 1.59% and has little relationship with the TOC content. So the total porosity in the Niutitang shale mainly comes from the mineral matrix pores. The FIB-SEM results have shown significant differences in the pore structure of the two shales.