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There are three sets of source rocks below the Changxing Formation in the southern Sichuan Basin, including the mud shale in Lower Silurian Longmaxi Formation, the argillaceous rock in Middle Permian, and the coal series in Upper Permian Longtan Formation. Many large and medium-sized gas fields have been discovered in the Changxing Formation, but the understanding of the source of natural gas is still unclear. The natural gas composition and carbon isotope analyses show that the natural gas of Changxing Formation in this area is mainly secondary gas (from crude oil cracking) and is characterized by high methane content and high dryness coefficient, which belongs to typical dry gas. Combined with the reservoir microscopic characteristics and the inclusion homogenization temperatures, a spatial-temporal model of hydrocarbon accumulation was constructed. The natural gas of Changxing Formation in the southern Sichuan Basin is mainly from a deep Silurian hydrocarbon source mixed with a small amount of coal series gas in the Longtan Formation. The reservoir in Changxing Formation did not capture the liquid hydrocarbon generated by the source rock at the peak of oil generation stages, so it mainly accumulates gas. The early and middle period of Yanshan Movement is the main period of gas accumulation, with partial accumulation in the Yanshanian-early Himalayan. The natural gas of Changxing Formation in the southern Sichuan Basin is different from that in the eastern Sichuan which is mainly from the coal series. The spatial-temporal timing is the key to effectively capture oil and gas in traps and determines the source and accumulation enrichment of oil and gas. It is the core of modern petroleum accumulation research to reveal the migration and accumulation process of oil and gas through history.