Silurian shale in Sichuan Basin is currently the most important target zone for shale gas exploration and development in China. Pore structure characteristics of Lower Silurian Longmaxi shales from southern Sichuan Basin were investigated. The combination of field emission scanning electron microscope (FE–SEM) and argon ion beam milling was utilized to describe the nanometer-to micrometer-scale (>1.2nm) pore systems. The shales were characterized by organic geochemical and mineralogical analyses. Total porosity, pore size distribution (PSD), specific surface area, and gas content were determined. Controls of organic matter richness, thermal maturity, and mineralogy on porosity were examined. The contribution of individual mineral components to total porosity was analyzed quantitatively. Total gas contents of the shales determined from canister desorption data were compared with theoretical (sorptive and volumetric) gas storage capacities.The total organic carbon (TOC) content of the shale samples ranges between 0.1 and 8.0 wt.% and helium porosity varies between 0.7 and 5.7%. Maturity in terms of equivalent vitrinite reflectance of bitumen (Reqv) ranges from 1.8 to 3.2%. TOC content is a strong control for the pore system of these shales, and shows a positive correlation with porosity. Porosity increases with increasing thermal maturity when Reqv is less than 2.5%, but decreases for higher thermal maturity samples. FE–SEM reveals four pore types related to the rock matrix that are classified as follows: organic matter (OM)–hosted pores, pores in clay minerals, pores of framework minerals, and intragranular pores in microfossils. Pores in clay minerals are always associated with the framework of clay flakes, and develop around rigid mineral grains because the pressure shadows of mineral grains prevent pores from collapsing. Pores of framework minerals are probably related to dissolution by acidic fluids, and the dissolution–related pores promote porosity of shales. A unimodal PSD exists in the micropore range of TOC–rich samples, while the PSD of carbonate–rich samples are bimodal. A PSD maximum in the micropore range is attributed by OM and another maximum in the range of mesopore–macropores is probably caused by the dissolution of carbonate minerals. Quantitative evaluation of the contribution of individual mineral components to porosity shows that the organic matter contributes approximately 62% to the total porosity. Framework minerals (quartz, feldspar, and carbonates, et al.) and clay minerals contribute 25% and 13%, respectively. The total gas content of these shales ranges from 0.4 to 6.2m3/t, and the total gas contents of selected samples determined from canister desorption tests agree with the theoretically estimated original gas-in-place (OGIP). OM-hosted pores are the main space for gas storage, and accounted for about 78% (55% adsorbed gas plus 23% free gas) of the OGIP, while pores in the inorganic matter accommodate 22% free gas of the OGIP.