The discovery of high-yield industrial gas flows in the limestone layer of the Permian Taiyuan Formation in the Ordos Basin highlights promising prospects for natural gas exploration and has positioned this region as a key exploration area. However, research on the origin and distribution of natural gas in the Taiyuan Limestone Formation, especially its hydrocarbon generation potential and whether these organically enriched limestones can serve as effective source rocks, remains limited. In this study, we aimed to analyse the composition and carbon isotopes of the Upper Palaeozoic Taiyuan Limestone Formation natural gas, including propane-specific isotopes. The isotopic data were compared with coal-type gases from the corresponding strata and oil-type gases from the Lower Palaeozoic carbonate strata. Natural gas in the Upper Palaeozoic Taiyuan Limestone Formation was markedly distinct from the ‘self-generated and self-accumulated’ oil-type gas in the Lower Palaeozoic subsalt strata, indicating no obvious correlation between the two gases. The results did not support the notion that large-scale natural gas accumulations in the Lower Palaeozoic carbonate formations could be originated from Upper Palaeozoic limestone source rocks. The natural gas in the Upper Palaeozoic Taiyuan Limestone Formation was highly consistent with the typical coal-type gas from the Upper Paleozoic. The geochemical characteristics of the natural gas in the region were consistent with that of conventional natural gas, the position-specific isotopic composition of propane ΔC−T values had a narrow, positive. This showed that the gas in the Taiyuan Limestone Formation was derived from type III kerogen, and propane mainly generated through the n-C3H7 free radical pathway. Geochemical analyses of the Taiyuan Limestone source rocks, such as the determination of total organic carbon, kerogen carbon isotopes, organic macerals. Combined with the geochemical analysis of natural gas, it revealed low abundance of organic matter but good kerogen types, predominantly type II–III, at a late to high-maturity evolution stage. Although the formation had certain hydrocarbon generation potential, it falls short of the hydrocarbon generation capacity of the Carboniferous–Permian coal measure source rocks. At present, there is no large–scale hydrocarbon generation, and it is not enough to provide hydrocarbon for the Lower Paleozoic