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In order to explore the characteristics of marine-continental transitional shale reservoir under overburden conditions, studies of organic geochemistry, mineral composition, parameters of pore structure and physical properties of shale in well Y4 of the Upper Permian Longtan Formation in the Puguang exploration area of northeastern Sichuan Basin were carried out. The shale of the Longtan Formation is characterized by high abundance of organic matter (ranging from 3.77% to 10.72%), humic and sapropelic organic matter (kerogen type of Ⅱ2 to Ⅲ) and post stage of maturation (%Ro values ranging from 3.82% to 3.97%). The average pore volume, specific surface area and porosity of shale are 0.047 mL/g, 31.8 m2/g and 6.64%, respectively. Reservoir space is mainly composed of organic pores, interlayer pores of clay minerals, dissolution pores of brittle minerals and micro fractures. The main pore structure is parallel plate-shaped pores and open tubular pores at both ends. The porosity of shale is positively correlated with the contents of TOC, pyrite and quartz in deep-water lagoon environment, which indicated that the original mineral composition and structure were controlled by anoxic reduction and stable water environment. Meanwhile, the effective complexation of rigid mineral particles with organic matter and clay minerals provided necessary conditions for the preservation of organic pores. Reservoir network is consisted of flat organic macropores affected by flattening transformation, densely-developed organic pores, intergranular pores and fractures of brittle minerals, and finally formed ultra-deep shale reservoir deposited in deep-water lagoon microfacies.