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The structural evolution and sedimentary differentiation of the Sichuan Basin in China are complex, with intricate reservoir pore structures that significantly impact shale gas production. This study examines the complexity and heterogeneity of the microscopic pore structures in the deep marine shale reservoir in the Longmaxi Formation. Pore structure characterization techniques are used to compare deep and shallow–medium marine shales, and siliceous and silty shales. The results reveal the factors influencing pore structure and their impact on exploration and development. The key points are as follows: (1) The pore structure of deep siliceous shale is the most complex due to its diverse range of pore development patterns, pore types, and sizes. (2) The box dimension of full pore size is about 1.52 for deep marine shale and 1.46 for shallow–medium shale. Organic matter (OM) content, the degree of pore development, and inorganic mineral content all correlate positively with the complexity of the pore structure in deep marine shale, which affects the formation of high-quality reservoirs. (3) Lateral heterogeneity of pore structures shows strong regional variations in the study area. Heterogeneity is more pronounced in the deep marine shale than in the medium and shallow shale formations. OM mesopores significantly influence the overall heterogeneity of the shale pore system. The deep marine shale reservoir is situated in an area with strong regional variations. The pore structure of high-quality reservoirs is more complex than those of shallow–medium marine shales, displaying notable heterogeneity. Pore structures with fractal dimension values close to that of the shallow–medium formations (box dimensions within 1.5) offer promising targets for the exploration and development of deep marine shale gas. [ABSTRACT FROM AUTHOR]