Thermochemical sulfate reduction (TSR) commonly occurs in carbonate–evaporite assemblages, making the identification of gas sources difficult. Given that the sources of natural gases in the Ordovician carbonate–evaporite assemblage of the Ordos Basin remain unclear, this study was conducted to reveal gas sources and TSR characteristics by geochemical and mineralogical analyses. The results showed that the C1/C1–5 and δ13C2 values of the Ordovician subsalt gases were higher than those only affected by thermal evolution owing to the selective consumption of the C2–5 components by TSR reaction. For some oil-type gases from the subsalt reservoirs, TSR even led to their δ13C2 values reflecting to the characteristic of coal-type gas. TSR-mediated reformation of methane in the Ordovician subsalt gases was extremely weak, and δ13C1 and δD1 values confirmed that it originated primarily from marine source rocks. Cracks and caves of the Ordovician subsalt reservoirs were generally filled with TSR-related secondary calcite, elemental sulfur, and pyrite, but little bitumen coexisted, indicating that the major reductants of TSR reaction were gaseous hydrocarbons, particularly the C2–5 components. Expulsion of liquid hydrocarbons from the Majiagou source rocks to form paleo-oil reservoirs was severely limited because the source layer had a low total organic carbon content and contained gypsum–salt rocks. Thus, the Ordovician subsalt gas reservoirs had primarily formed through the direct migration and accumulation of gaseous hydrocarbons. Consequently, the primary gas reservoirs are the main targets for future natural gas exploration in the Ordovician carbonate–evaporite assemblage of the Ordos Basin.