Compositions of non-hydrocarbon and noble gases in natural gas samples collected from the Kuqa Depression, Tabei Uplift Belt, North Depression, Tazhong Uplift, and Southeast Depression in the Tarim Basin, China were analyzed to investigate the origin of the natural gases. The results show that the largest component of the natural gases is hydrocarbon gas with a concentration of 33.46% to 99.26%. The non-hydrocarbon gases are mainly composed of CO2 and N2 with concentrations of 0.01% to 17.95% and 0.1% to 52.45%, respectively. The helium content varies from 0.005% to 0.30%. The 3He/4He ratio varies from 0.01 Ra to 0.55 Ra (where Ra denotes atmospheric 3He/4He ratio = 1.4 × 10–6), and the 4He/20Ne ratio varies from 8.3 to 7400. Most of the 3He/4He values are below 0.1 Ra. The low 3He/4He ratios indicate crustal radiation to be the main source of the helium. There are no positive correlations between the 3He/4He ratio and helium abundance, non-hydrocarbon abundance, heat flow, and the age of reservoir formations. The ratios of 3He/4He are related to the time or stage of the natural gas accumulation. The ratios of 3He/4He in the reservoirs that were filled in the later stage (Himalayan period) are lower than those in the reservoirs that were filled in the earlier stage (Yanshan period).