The Lower Sinian Doushantuo Shale comprises the oldest Neoproterozoic shale gas reservoir in the Middle Yangtze Yichang area of China, which makes the study of their pore characteristics critical to future shale gas exploration and exploitation. Geochemical, petrographical, and pore characteristics are studied in detail, with focused ion beam scanning electron microscopy (FIB-SEM) image analysis to further support and confirm the interpretations of the nano-scale pore structure characteristics. High total organic carbon (TOC) content, high thermal maturity, and considerable brittle mineral content indicate promising potential of the Doushantuo shale. High TOC samples suggest elevated micro-meso porosity, and H2(b) and H3 type hysteresis loops indicate inkbottle, slit-like, and flake-like pore types. Significant inorganic pores are commonly observed in dolomite, pyrite, and apatite, which are characterized by diamond or irregular shapes, with pore diameters ranging from 5 nm to 1000 nm as a result of the interaction between the minerals and the acidic organic fluids. Clustering organic matter (OM) pores are observed with pore diameters ranging from 5 nm to 50 nm; they are characterized by sponge-like, elliptical, and alveolate shapes, which indicate minor organic matter (OM) pores. More substantial organic matter (OM) pores can also be found around or between the pyrite and apatite. Fractures can be clearly observed between the organic matter and minerals with lengths of approximately 10 μm and 50 nm in width, which serve as conduits for shale gas migration. The pores in the Doushantuo Shale are dominated by inorganic pores and minor organic matter (OM) pores, which are different from the pore structure of the Wufeng-Longmaxi Shales in the Sichuan Basin. The Doushantuo Shale organic matter (OM) pores are much smaller and more densely distributed than those in the Wufeng-Longmaxi Shales. The different organic matter origins of these two shales have caused distinct organic matter (OM) pore-development mechanisms. Organic matter (OM) pores and inorganic pores could contribute to the volume of the adsorbed gas and free gas, respectively, which provide significant reservoir space in the Lower Sinian Doushantuo Shale in the Yichang area.