Explorations of Carboniferous petroleum system mainly focuses on the source rocks of the Upper Carboniferous Batamayineishan Formation. In contrast, the validity of the theoretically better- developed source rocks of the Lower Carboniferous Dishuiquan Formation is still inconclusive. Meanwhile, the frequent Carboniferous volcanism in the basin possesses the geological background for generating abiogenic alkane gas, but there are few related studies. Based on the molecular and stable carbon isotopic compositions of natural gas from the Dongdaohaizi- Wucaiwan sag and Baijiahai uplift in the eastern Junggar basin, this study systematically analyzed its genetic origin and potential secondary alteration and identified four different types of natural gases: ① coal- derived gas from the Dishuiquan Formation; ② coal- derived gas from the Batamayineishan Formation; ③ abiogenic methane mixed with thermogenic alkane gas; ④ leaked thermogenic gas. These results confirm the validity of the Lower Carboniferous source rocks in the eastern Junggar basin and also identify traces of abiogenic alkane gas, which opens up a new field of gas exploration in the deep and ultra- deep basin and also provides a typical case of identifying “homogeneous and hetero- origin” gas.