Deep shale has the characteristics of large burial depth, rapid changes in reservoir properties, complex pore types and structures, and unstable production. The whole-rock X-ray diffraction (XRD) analysis, reservoir physical property parameter testing, scanning electron microscopy (SEM) analysis, high-pressure mercury intrusion testing, CO2 adsorption experimentation, and low-temperature nitrogen adsorption–desorption testing were performed to study the pore structure characteristics of marine shale reservoirs in the southern Sichuan Basin. The results show that the deep shale of the Wufeng Formation Longyi1 sub-member in the Luzhou area is superior to that of the Weiyuan area in terms of factors controlling shale gas enrichment, such as organic matter abundance, physical properties, gas-bearing properties, and shale reservoir thickness. SEM is utilized to identify six types of pores (mainly organic matter pores). The porosities of the pyrobitumen pores reach 21.04–31.65%, while the porosities of the solid kerogen pores, siliceous mineral dissolution pores, and carbonate dissolution pores are low at 0.48–1.80%. The pores of shale reservoirs are mainly micropores and mesopores, with a small amount of macropores. The total pore volume ranges from 22.0 to 36.40 μL/g, with an average of 27.46 μL/g, the total pore specific surface area ranges from 34.27 to 50.39 m2/g, with an average of 41.12 m2/g. The pore volume and specific surface area of deep shale gas are positively correlated with TOC content, siliceous minerals, and clay minerals. The key period for shale gas enrichment, which matches the evolution process of shale hydrocarbon generation, reservoir capacity, and direct and indirect cap rocks, is from the Middle to Late Triassic to the present. Areas with late structural uplift, small uplift amplitude, and high formation pressure coefficient characteristics favor preserving shale gas with high gas content and production levels.