Shale gas exploration and development in the Luzhou area continues to expand into deeper regions, yet a systematic understanding of the pore structure characteristics and gas-bearing properties of the deep shale reservoirs in this area remains lacking, which constrains the scientific extraction of deep shale gas in the region. Taking the deep shale of the Longmaxi Formation in the Luzhou block of the southern Sichuan Basin as the research object, comprehensive research methods such as FE–SEM, FIB–SEM three-dimensional reconstruction technique, LPCO₂A, LTN₂A, and methane isothermal adsorption experiments were employed to systematically study the pore structure characteristics and gas-bearing properties of the deep shale in the Longmaxi Formation. The research results show that the pores of the deep shale of the Longmaxi Formation are mainly composed of organic pores, intragranular dissolution pores, and interlayer pores of clay minerals, and organic pores are primarily isolated with poor connectivity. The PV of the shale is mainly contributed by mesopores, and the SSA is mainly contributed by micropores. The pore structure of the Long 1₁³ layer shale is the most developed. The D2 value is greater than the D1 value, indicating that the pore space structure of deep shale is more complex than its pore surface. The increase in TOC and quartz content appears to favor the development of pores and enhance reservoir homogeneity, while the increase in clay mineral content appears to inhibit pore formation and enhance heterogeneity. Micropores serve as the primary host for adsorbed gas, while mesopores serve as the primary host for free gas.