Although the Fukang Sub-depression is the largest hydrocarbon generation depression in the Junggar Basin and promises favorable potential for oil and gas exploration, only several small–medium oil/gas accumulations have been discovered so far. After analyzing the molecular and stable carbon isotopic compositions of natural gases and its associated low molecular weight hydrocarbons (LMWHs) from eastern Fukang Sub-depression, their genetic types and origins are discussed in this study. Natural gases are wet gases with an average dryness coefficient of 0.84. Stable carbon isotopes of methane and ethane are well correlated with the thermal evolution trend of coal-derived gases. The C5–7 LMWHs are enriched in methyl cyclohexane but they lack n-alkanes, indicating a predominance of higher plant input. Gases have maturities ranging 0.76%–0.93%Ro and are well consistent with their low n-heptane (H) and iso-heptane (I) contents. The geochemical characteristics of natural gases from eastern Fukang Sub-depression are quite similar with those from the Turpan–Hami Basin. Their gases are considered to be low-mature gases derived from the Lower–Middle Jurassic coal measures. In contrast, they show remarkable differences with those from the Wucaiwan gas field; they are considered to have high-mature gases derived from the Carboniferous coal measures.