Based on drilling cores, well logging and seismic data, source rocks and reservoirs are evaluated; and the natural gas genesis is identified through the analysis of natural gas isotopes, components and fluid inclusions, to study the gas accumulation conditions of the gypsum salt rock related strata of the Ordovician lower assemblage in Ordos Basin. (1) The natural gas from Ordovician lower assemblage is high thermal evolution dry gas from marine source rock, characterized by relatively light δ13C value of methane and heavy δ13C value of ethane. The natural gas is identified as gas cracking from crude oil according to component analysis. Thermochemical sulfate reduction (TSR) reaction has happened between the hydrocarbon fluid and sulfate as sulfur crystals are found in the cores, hydrogen sulfide is found in the natural gas, and hydrocarbon and hydrogen sulfide fluid inclusions are widespread in secondary minerals. (2) Around the gypsum-salt lows, argillaceous rocks are extensive in the Ordovician lower assemblage, reaching a cumulative thickness of 20–80 m. The effective source rocks include argillaceous rock rich in organic laminae, algal clump and algal dolomite. Analysis shows that the source rocks have a dominant TOC of 0.1%–0.5%, 0.31% on average and 3.24% at maximum. The source rocks have an average TOC of 0.58% after recovered through organic acid salt method, indicating the source rocks have high hydrocarbon supply potential. (3) In the sedimentary period, the palaeo-uplift controlled the distribution of reservoirs. The inherited secondary palaeo-uplift in Wushenqi–Jingbian east of the central palaeo-uplift and the low uplift formed by thick salt rocks near Shenmu–Zizhou area controlled the distribution of penecontemporaneous grain shoal dolomite reservoirs. The salinization sedimentary environment of gypsum salt rock can promote the development of reservoir. There are three types of dolomite reservoirs, the one with intercrystalline pore, with dissolution pore, and with fracture; intercrystalline and dissolution pores are main reservoir spaces. (4) There are two types of cap rocks, namely tight carbonate rock and gypsum-salt rock, constituting two types of source-reservoir-cap assemblages respectively. The general accumulation model is characterized by marine source rock supplying hydrocarbon, beach facies limy dolomite reservoir, small fractures acting as migration pathways, and structural-lithologic traps as accumulation zones. (5) The third and fourth members of Majiagou Formation are major target layers in the lower assemblage. The Wushengqi–Jingbian secondary paleo-uplift area and Shenmu–Zizhou low uplift are dolomite and limestone transition zone, there develops tight limestone to the east of the uplift zone, which is conducive to the formation of gas reservoir sealed by lithology in the updip. Two risk exploration wells drilled recently have encouraging results, indicating that the two uplift zones are important prospects.