Large amounts of natural gas have been discovered recently, both in carbonate reservoirs and in shales in the Sinian–Silurian strata of the Sichuan Basin, southern China. Although numerous studies have been conducted to learn about the accumulation of conventional and shale gas, the gas generation history, the origins of the two types of gas, and gas resources in the basin remain unclear. In this study, the hydrocarbon generation histories of Cambrian and Silurian source rocks were reconstructed on the basis of thermal history and hydrocarbon generation kinetic parameters. Intensive cracking of crude oil to generate considerable amounts of secondary cracking gas in Silurian and Cambrian formations occurred during deep burial. The high abundance of overmature pyrobitumen in carbonate reservoirs and shale demonstrates the occurrence of large-scale in situ cracking of liquid hydrocarbons. A mixing model was proposed to quantitatively determine the contribution of kerogen and oil-cracking gas in shale gas accumulations. The mixing of two thermogenic gases with different maturities resulted in a reversal and a rollover of the carbon isotope compositions of shale gas. Moreover, gas resources from the cracking of three occurrence states of liquid hydrocarbons—including dispersed residual bitumen in source rocks, dispersed oil outside the source, and accumulated oil in reservoirs—were evaluated in Sinian–Cambrian and Silurian petroleum systems in the Sichuan Basin, providing a guide for future deep gas exploration of similar formations in China and elsewhere.