The source of the natural gas in the Lower Paleozoic Ordovician strata in the Ordos Basin, China is a controversial issue. In the present study, the genesis and distribution characteristics of the Ordovician natural gas were qualitatively investigated based on the composition of the natural gas and the hydrocarbon isotopic composition. Then, the kinetics of the carbon isotope were analyzed to determine the proportions of the gas in the Ordovician gas reservoir contributed from the Carboniferous-Permian and Ordovician strata. The results show the following. Compared to the Upper Paleozoic natural gas, the Ordovician natural gas has a large dryness coefficient. In core areas where gypsum-salt rocks are developed, the gypsum-salt rocks completely isolate the gas sources. The weathering crust of the reservoir in the fifth member of the Majiagou Formation (Ma51+2) originates primarily from the Upper Paleozoic coal-measure source rocks, while the Ma55 and the pre-salt natural gas are mainly derived from the Ordovician source rocks. In the areas where the gypsum-salt rocks are relatively well-developed, the gypsum-salt rocks isolate the gas source to some extent, the pre-salt gas reservoir is mainly derived from the Lower Paleozoic source rocks, and this contribution gradually increases with increasing depth. In the areas where the gypsum-salt rocks are not developed, the proportion of the contribution of the Upper and Lower Paleozoic source rocks to the gas source of the Ordovician gas reservoir is mainly controlled by the volume of gas generated and the other accumulation conditions, and it does not reflect the isolation effect of the gypsum-salt rocks on the gas source. The Ordovician natural gas accumulation models in the central-eastern Ordos Basin can be divided into four types according to the differences in the gas sources.