The black shale of the Upper Ordovician and Lower Silurian is a significant target for shale gas exploration in the Southern Sichuan Basin. In this study, we introduced a lithofacies classification for shale based on rock mineral composition. Because the pore structure of gas shale reservoirs are complex and greatly affect the gas storage and transport in shale, four different methods of low-pressure nitrogen gas adsorption, high-pressure mercury intrusion, scanning electron microscopy (SEM) and gas expansion methods were used to investigate the reservoir pore structure and storage space. Combined with X-ray diffraction, total organic matter content (TOC), gas content, methane adsorption, porosity and permeability and wireline data, the key factors that affect shale gas content and storage of shale gas were analyzed.According to our shale classification, three main lithofacies, i.e., calcareous mudstone (CM), high calcareous mixed mudstone (HCMM) and low calcareous mixed mudstone (LCMM), were identified in our study area. The experiment indicates that the shale has a high TOC, thermal maturity and gas content. The methane adsorption isotherms show that the sorbed gas content has a positive correlation with TOC. Difference of TOC between the three is small. Nitrogen adsorption indicates that mesopores dominate the shale pore composition and organic matter is the main source of mesopores. Mercury injection shows that the macropore volume accounts for approximately 14–22% of the total pore volume. No obvious pore structure differences were found for different lithofacies. However, taking the porosity into consideration, LCMM has the largest macropore volume. The SEM observations revealed that organic matter pores, interparticle pores and intraparticle pores are the main pore types. Interparticle pores mainly develop in LCMM which has a relatively high quartz and low carbonate content, it may be the major reason for high porosity, high macropore volume, and high free gas content of LCMM. Free gas and absorbed gas are the major storage form of shale gas. Given similar temperature and pressure conditions, the total organic matter content is the major factor that affects the adsorbed gas content. Therefore, with high free gas and adsorbed gas content, LCMMs with high total organic matter contents would be the most favorable type of lithofacies in this region.