A systematic comparative analysis of shale reservoir characteristics of the Wufeng-Longmaxi (O3w-S1l) and Niutitang (Є1n) Formations in southeastern Sichuan Basin and its neighboring areas was conducted with respect to mineralogy, organic geochemistry, pore structure, methane sorption, brittleness, and fractures. Results indicate that (1) organic matter (OM)-hosted pores that are hundreds of nanometers to micrometers in size in the Longmaxi shale are well-developed in migrated OM rather than in the in situ OM, and they are the dominant reservoir spaces. Furthermore, the total organic carbon (TOC), brittleness, organic pores, and bedding fractures have good synergistic development relationships. However, there are fewer OM-hosted pores in the Niutitang shale; they are smaller in size, usually less than 30 nm, and have a more complicated pore structure. The intergranular pores in cataclastic organic-inorganic mineral fragments are the dominant reservoir spaces in the Niutitang shale and are coupled with stronger methane sorption and desorption capacities. (2) The piecewise correlation between TOC and brittleness indicates the significant differences in pore and fracture characteristics. When the TOC , the TOC, brittleness, organic/inorganic pores, and fractures synergistically develop; when the TOC , even though the increase in ductility reduces the number of fractures, the lower cohesive strength, internal friction angle, and weaker surfaces of interlayer fractures and cataclastic minerals promote the development of slip fractures, which significantly improves the fracture effectiveness and reservoir spaces for free and absorbed shale gas. (3) The Longmaxi, Wufeng, and Niutitang shales formed and evolved in different evolutionary stages. With the evolution of hydrocarbon generation, diagenesis, tectonic deformation, and pressure, the size and proportion of OM-hosted pores gradually decrease. At the same time, the complexity of the pore-fracture structure, the methane adsorption/desorption capacity, and the proportion of inorganic pores and fractures increase.