Various shale lithofacies differ significantly in terms of gas content and pore structure characteristics. In this study, FE-SEM, low-pressure gas adsorption (LPGA), in-situ reservoir water saturation restoring, and high-pressure (0–51Mpa) methane adsorption were conducted to systematically characterize pore structure and evaluate the gas content of different shale lithofacies in the Wufeng-Longmaxi Formation, southern Sichuan Basin. The mineral compositions identified four shale lithofacies, and pores are abundant in siliceous shale and mixed shale. Siliceous shale has the largest pore volume (PV) and specific surface area (SSA), averaging 0.0310 cm³/g and 25.827 m²/g, respectively. However, the PV and SSA are lowest in argillaceous shale, averaging 0.0217 cm³/g and 18.734 m²/g, respectively. Water saturation is positively correlated with clay minerals, and argillaceous shale possess the highest water saturation of 60% due to the highest clay content. The supercritical Dubinin-Astakhov (S-DA) excess adsorption model predictions deviated less from the measured data and fitted well. The shale adsorption capacity are dominated by TOC content and total SSA. However, water and temperature have an inhibitory activity on adsorption capacity, with the adsorption capacity of water-bearing shales decreasing by 28%∼81% at a water saturation of 30%∼65% compared to dry shales. As the temperature increased from 40 °C to 80 °C, the methane adsorption capacity decreased from 3.95 to 2.79 m³/t, a 29% decrease. The shale gas content prediction models were established and extrapolated into the functions of reservoir depth. Deep shale gas reservoirs are dominated by free gas, accounting for over 90% at 5000 m. Siliceous shale has the highest gas content, followed by mixed shale, argillaceous-siliceous shale, and argillaceous shale. It is estimated that siliceous shale has a three-fold higher gas content than argillaceous shale. Siliceous and mixed shale are favorable reservoirs for shale gas exploration and development due to their high gas contents and low water saturation.