Abstract: A large set of thick lacustrine organic-rich shale is developed in the second member of Paleojene Funing Formation (Fu-2 member) in Gaoyou Sag, Subei Basin. It is of great theoretical significance for shale oil exploration to clarify the differential development mechanisms of shale reservoir structures in different organic-rich lithofacies. Large-area scanning electron microscopy (MAPS) analysis, CT scanning, and focused ion beam scanning electron microscopy (FIB-SEM) were used to analyze the pore and fracture structure characteristics of shales with different lithofacies of Fu-2 member in the Subei Basin. It was found that the Fu-2 member in Subei Basin mainly developed three types of high-quality shales: calcareous dolomitic shale, felsic-calcareous dolomitic shale, and felsic-argillaceous shale, with significant differences in mineral composition and sedimentary structure. Overall, the types of pores and fractures could be divided into organic pores and fractures, intergranular pores, dissolution pores (carbonate minerals and K-feldspar), and inorganic fractures. The results showed that mineral compositions and structural characteristics were the main controlling factors affecting the development of pore and fracture structures in the three high-quality shale lithofacies of Fu-2 member in Subei Basin. Carbonate mineral dissolution pores and inorganic fractures accounted for the highest proportions in calcareous dolomitic shale. Felsic intergranular pores and inorganic fractures had the highest proportions in felsic-calcareous dolomitic shale. Felsic intergranular pores and clay mineral inorganic fractures had the highest proportions in felsic-argillaceous shale. Influenced by diagenesis, the dissolution pore size and pore-forming efficiency of carbonate minerals (calcite and dolomite) in calcareous dolomitic shale were higher than those in felsic-argillaceous shale. In addition, the main lamina types developed in the laminated shale of the study area included felsic lamina, carbonate mineral lamina, and argillaceous lamina, with surface porosity decreasing successively in this order. The laminated shale promotes the development of a large number of horizontal laminae fractures, providing more favorable channels for the migration of organic acids, resulting in higher dissolution pore size and pore-forming efficiency compared to laminated or massive shale.