The lower Permian series in northwestern Sichuan basin of China is a favorable region for natural gas accumulation with several potential source rocks and high-quality reservoirs. However, the tectonic evolution in this area has gone through long-term and complicated activities and the origin of gases in the lower Permian series is complex. For the wise exploration strategies planning, the origin and accumulation of natural gas in lower Permian reservoir have been addressed. And the results reveal that: (1) Three sets of potential source rocks, including the mudstone of Lower Cambrian Qiongzhusi formation, Lower Silurian Longmaxi formation and the marine carbonate source rocks of Lower Permian, have been identified as the gas sources in Lower Permian reservoirs. (2) The gases mainly contain by hydrocarbon gases, with the ratio of C1/C2+ > 0.99, and the characteristics of carbon isotopes are various and several wells’ are reversed or close to reversed. The δ13C2 values of Hewanchang and Wujiaba gas fields are ranging from −33.35‰ to −36.34‰(PDB), similar to the production of sapropelic organic matter. The Shuangyushi and Kuangshanliang gas fields, with the δ13C2 values ranging from −28‰ to −30‰(PDB), are source mixed gas. And the δ13C2 values of Jiulongshan gas field are the heaviest with the value range from −25.23‰ to −28.4‰(PDB). (3) The biomarkers of reservoir extracts are consistent with those of the lower Permian source rock, but the bitumen scales in lower Permian are not as much as those in the lower Cambrian or Lower Silurian series, which reveals that the crude oil creaked gas formed in lower Permian series falls a great deal than that in Cambrian and Silurian series. Based on the comprehensive researches of natural gas composition, carbon isotope, biomarkers of extract and other parameters, the natural gases in lower Permian series are mixed by the crude oil creaked gas from deep formation and the lower Permian source rock, and the scale of fracture determines the amount of creaked gas mixed in the lower Permian reservoir.