The Tiangongtang area in southern Sichuan Basin is a shale gas exploration and development hotspot, famous for the development of large-scale marine deposits with good sedimentary stability and continuity. Focusing on the laminated organic-rich shale of the Wufeng-Longmaxi Formations, this paper clarifies the shale lamination types based on core description and microscopic observation of large and thin sections. By means of geochemical, mineralogical, petrograpic and pore structural analyses and field emission scanning electron microscope observation, the pore structure and reservoir physical properties are revealed. Accordingly, the internal structural differences and control mechanisms of different lamination combinations are revealed. Shales of the Wufeng-Long1-1 submember mainly develops three lamination combinations: graded, massive and sand-mud interbedded. Graded laminated and interlaminated shale assemblages have much higher horizontal permeability than the massive while the latter has the highest vertical permeability; the graded has the best reservoir physical properties. Moreover, the pore volume and specific surface area of fractures show a decreasing trend from the graded to massive to interlaminated. Under the control of sedimentary environment and diagenesis, graded laminated shales with higher TOC and organic-clay laminae have larger effective pore space, higher pore connectivity and larger pore volume than the interlaminated with lower TOC and thick silty and clay laminae. With relatively high organic content and disordered porous media massive shales have better quality effective storage spaces than sand-mud interbedded shales but worse quality than graded laminated shales.