The Wumaying buried hill experienced multi-stage tectonic movements, which resulted in a complicated and unclear nature of the hydrocarbon accumulation process. To solve these problems, in this study—based on the structural evolution and burial–thermal history of the strata, using petrology, fluid inclusion microthermometry, geochemical analysis of oil and gas, Laser Raman spectrum, and fluorescence spectrum—the history of hydrocarbon charging was revealed, and the differences in hydrocarbon charging of different wells was clarified. The results indicate that the only source for Permian oil and gas reservoirs are Carboniferous–Permian coal-measure source rocks in the Wumaying buried hill. There are three periods of hydrocarbon charging. Under the channeling of faults and micro cracks, low-mature oil and gas accumulation was formed in the first period, and the accumulation time was 112–93 Ma. In the late Cretaceous, a large-scale uplift exposed and damaged the reservoirs, and part of the petroleum was converted into bitumen. In the middle–late Paleogene, the subsidence of strata caused the coal-measure to expel mature oil and gas, and the accumulation time of mature oil and gas was 34–24 Ma. Since the Neogene, natural gas and high-mature oil have been expelled due to the large subsidence entering the reservoir under the channeling of active faults; the accumulation time was 11–0 Ma. The microfractures of Permian reservoirs in the Wumaying buried hill are the main storage spaces of hydrocarbons, and the fractured reservoirs should be explored in the future. The first period of charging was too small and the second period was large enough in the WS1 well, resulting in only a late period of charging in this well.