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The difference in quartz types in shales not only affects the porosity and permeability of the rocks, but also reflects the difference in the sedimentary environments. We established the formation mechanism and numerical model of quartz in shales of Wufeng and Longmaxi formations in the Wangjiawan Section, South China, based on thin-section studies using SEM (scanning electron microscope), SEM-CL (cathodoluminescence), XRD (X-ray diffraction) and geochemical analyses. There are two types of quartz in the shales: detrital quartz and authigenic quartz. Detrital quartz is mostly silt-size, typically ranging from 10 to 60 μm in size and subangular to angular monocrystal in shape, and brighter than authigenic quartz by CL intensity; authigenic quartz is present in two phases in shape: grain overgrowths and crystallite grains. Overgrowth surfaces are subhedral. Crystallite grains are typically less than 10 μm in size, euhedral or subhedral monocrystal in shape. Authigenic quartz can be subdivided into biogenic quartz and clay mineral transformed quartz according to the source of silicon. In the numerical model, the content of detrital quartz is relatively consistent (20％); the content of biogenic quartz ranges from 40％ to 70％, with a sharp fall (0–30％) in the Guanyinqiao mudstone. During the Katian, a lower anoxic and dense water column make the dissolution of biogenic silica well preserved. Biogenic quartz is the major contributor to the sediment. During the Early Hantian interval, due to the drop of sea level and the oxygenation of seafloor, the sediment is mainly composed of clay transformed quartz and detrital quartz. During the Latest Hatian and Rhuddanian, rapid sea level rise and anoxic ocean enhance the preservation of the biogenic silica, thereby biogenic quartz re-emerges as the major contributors to the sediment. Authigenic crystallite grains and grain overgrowths have filled in primary pore space and have decreased the interparticle porosity, however, as a rigid framework, they can suppress compaction and maintain the intal pore structure. The formation of authigenic quartz results in the increase of total quartz, which fortifies the brittleness of rocks and is beneficial to the development of shale gas.