The Wufeng Formation–Longmaxi Formation in the Sichuan Basin in South China is the key stratum for shale gas exploration and production. To date, three national shale gas demonstration zones have been developed. Nevertheless, there are still some test wells that have not yet been commercialized. In this study, the geological characteristics of commercial and non-commercial zones are analyzed, as are the main controlling factors of high-producing wells (high estimated ultimate recovery; EUR), and the reasons for low-production wells (low EUR) by dissecting the three national shale gas demonstration zones and the main shale gas exploration wells. The results of this study indicate the following: (1) The black shale in the WF2–LM4 graptolite zone is deposited in the Craton depression on the Upper Yangtze plate, which provides a relatively stable tectonic environment for tectonic deformation and uplift destruction. The large shale thickness and weak tectonic activity jointly result in shale gas being enriched mainly in the deep-water shelf. (2)The regional fault has a destructive effect on shale gas preservation, and the shale gas reservoir is likely to be destroyed. In the areas close to the regional fault, multiple fracture-fluid migration activities caused by multistage tectonic movements are also detrimental to shale gas preservation. Conversely, shale gas is generally well preserved in areas far from regional faults. (3) The black shale thickness in the WF2–LM4 graptolite zone in the deep-water shelf area controls the shale gas field distribution. Furthermore, the horizontal well trajectory in the WF2–LM4 graptolite zone determines the shale gas well test production and EUR. The results of this work will provide a reference for shale gas exploration and development of the Wufeng Formation–Longmaxi Formation in the Sichuan Basin, as well as the Silurian strata in other parts of the world.