Abstract: The deep-water area of the Qiongdongnan Basin has become a hotspot for natural gas and gas hydrates exploration in the northern South China Sea. Although exploration and research on deep-water oil and gas as well as gas hydrates continue to advance, controversies remain regarding gas sources and genetic types of gas hydrates. the characteristics of low-molecular-weight alkane gases in conventional gas reservoirs and hydrate reservoirs within the Qiongdongnan Basin were systematically compared, key mechanisms controlling hydrocarbon gas composition and carbon isotopic fractionation were analyzed, and an identification model was established. Results demonstrate that during vertical migration of thermogenic hydrocarbon gases from mid-deep layers to shallow formations in the Qiongdongnan Basin, significant compositional and isotopic fractionation occurred: δ¹³C₁ values decreased notably while C₁/C₂ ratios increased substantially, showing potentially biogenic-like pseudomorphism. These pseudobiogenic hydrocarbon gases can still form stable hydrates in gas hydrate stability zones, resulting in the uncertainty in identifying hydrate hydrocarbon origins. By proposing a novel perspective differentiating “Diffusion–Leakage” mechanisms, this study provided a scientific approach for determining gas sources of gas hydrates, holding significant implications for further clarifying gas hydrates accumulation patterns and evaluating resource potential.