Investigations into the connectivity and complexity of pore systems in shales are essential for understanding the flow of shale gas and the capacities of the associated reservoirs. In the present study, eight shale samples from the Wufeng-Longmaxi (WF-LMX) Formation that were collected from Well Yucan-6 in the southeast of the Sichuan Basin were analyzed for microstructural, pore network, and pore connectivity characteristics. The measurement results of low-pressure nitrogen adsorption illustrated that all shale samples contain micropores, mesopores, and macropores. Micropores and mesopores account for a high proportion of the total pores, and the dominant pore throat size is in the range of 2–6 nm. High-pressure mercury injection tests reveal that the porosity, total pore volume, and total specific surface area of pores for samples from the WF Formation are higher than those for samples from the LMX Formation. In spontaneous absorption experiments, the slopes of the absorption curves of n-decane (oil-wetting) and deionized water (water-wetting) in the WF and LMX Formations varied from 0.254 to 0.428 and from 0.258 to 0.317, respectively. These results indicate that shales in both formations exhibit mixed wettability characteristics, but lipophilic pores are better connected relative to hydrophilic pores. The total organic carbon and silica contents are the main factors controlling the pore connectivity in these shales, while the effects of other minerals are not significant. The findings of this work can improve our understanding of the pore structure characteristics of black shale.