The lower Silurian Longmaxi Formation shale in the Sichuan Basin is one of the most promising shale gas plays in China. Pore structure has a significant impact on hydrocarbon migration within shales. This study conducts systematic experiments to analyze the pore structure, wettability, and methane adsorption capacity of the Longmaxi Formation shale samples from the southern Sichuan Basin. The pore-size distributions obtained from N2 adsorption, high-pressure mercury intrusion porosimetry, and statistical analysis of representative field emission–scanning electron microscopy photographs of organic matter (OM) are compared to evaluate the contribution of OM pores to total pore spaces. Shale wettability was determined by contact angle measurements and spontaneous imbibition experiments. The results reveal that these samples could be divided into three wettability categories: more water-wet samples Z1, more oil-wet samples Z4, and intermediate-wet samples Z2 and Z3. Although samples Z1 and Z4 have similar total organic carbon (TOC) contents, OM pores within sample Z4 have a larger average pore size and occupy a greater proportion of the total pore spaces compared with sample Z1, whereas inorganic pores contribute more to the total pore spaces of sample Z1. Sample Z4 has a larger methane adsorption capacity than sample Z1 with a higher Brunauer–Emmett–Teller (BET) surface area, which may be caused by the difference in their OM pore types. Samples Z2 and Z3 with less TOC content have lower porosities and BET surface areas as well as lower methane adsorption capacities. Consequently, the pore structure significantly affects the wettability and methane adsorption capacity of the Longmaxi shale.