Abstract The petrophysical characteristics of unconventional reservoirs have significant impacts on hydrocarbon storage and transport. In this study, 26 shale samples with various lithofacies from Lower Silurian Longmaxi shales in the Jiaoshiba area of Sichuan Basin are investigated. The pore network (morphology, porosity, and pore structure parameters) is comprehensively characterized using scanning electron microscopy, helium pycnometry, and low-pressure gas adsorption techniques. Permeability coefficients are derived from pulse-decay measurements on parallel to bedding samples. Geological controls on the pore shape, porosity, pore size, pore size distribution, and permeability of the shales are analyzed, and quantitative relationships with which to estimate the permeabilities and pore-throat apertures controlling gas flow are developed. Three general lithofacies are summarized in view of their mineralogy: siliceous, argillaceous/siliceous mixed, and argillaceous shales. Pore structure parameters (porosity, specific surface area, and pore volume) show positive correlations with total organic carbon (TOC) content. Organic matter-hosted pores contribute to approximate 67% of the porosity of siliceous shales, while inorganic matter contributes to 55% of the porosity of argillaceous shales. Klinkenberg-corrected permeabilities range between 0.01 and 46.4 μD, and are controlled by the alignment of clay flakes. Negative relationships exist between TOC content, porosity, and permeability values. Siliceous shales generally have the lowest permeabilities, whereas the argillaceous shales with developed oriented clay flakes have relatively high permeabilities. The seepage-pore apertures, estimated using the Winland correlation, range from 9 to 476 nm. These values are much higher than those obtained from nitrogen adsorption analysis (adsorption-pore apertures). A power correlation exists between seepage-pore apertures and total clay minerals content of shales studied. A fracture model (sheet) is used to predict absolute permeability based on seepage-pore apertures. The predictions are reasonable, and justify the application of the sheet model and seepage-pore apertures. The siliceous shales are featured by a high TOC content, large porosity and specific surface area, and low permeability, which are favorable to gas preservation.