The Weiyuan (WY) and Changning (CN) fields are the largest shale gas fields in the Sichuan Basin. Though the shale gases in both fields are sourced from the Longmaxi Formation, this study found notable differences between them in molecular composition, carbon isotopic composition, and noble gas abundance and isotopic composition. CO2 (av. 0.52%) and N2 (av. 0.94%) were higher in Weiyuan than in Changning by an average of 0.45% and 0.70%, respectively. The δ13C1 (−26.9% to −29.7%) and δ13C2 (−32.0% to −34.9%) ratios in the Changning shale gases were about 8% and 6% heavier than those in Weiyuan, respectively. Both shale gases had similar 3He/4He ratios but different 40Ar/36Ar ratios. These geochemical differences indicated complex geological conditions and shed light on the evolution of the Lonmaxi shale gas in the Sichuan Basin. In this study, we highlight the possible impacts on the geochemical characteristics of gas due to tectonic activity, thermal evolution, and migration. By combining previous gas geochemical data and the geological background of these natural gas fields, we concluded that four factors account for the differences in the Longmaxi Formation shale gas in the Sichuan Basin: a) A different ratio of oil cracking gas and kerogen cracking gas mixed in the closed system at the high over-mature stage. b) The Longmaxi shales in WY and CN have had differential geothermal histories, especially in terms of the effects from the Emeishan Large Igneous Province (LIP), which have led to the discrepancy in evolution of the shales in the two areas. c) The heterogeneity of the Lower Silurian Longmaxi shales is another important factor, according to the noble gas data. d) Although shale gas is generated in closed systems, natural gas loss throughout geological history cannot be avoided, which also accounts for gas geochemical differences. This research offers some useful information regarding the theory of shale gas generation and evolution.