Investigating the primary influencing factors that regulate the enrichment of shallow gas not only deepens our understanding of the rules governing shallow gas enrichment in deep-ocean environments but also has the potential to enhance the success rate of locating shallow gas reservoirs. Recent drilling activities in the LS36 gas field located in the central Qiongdongnan Basin have revealed a substantial shallow gas reserve within the sediments of the Quaternary Ledong Formation, marking it as the first shallow gas reservoir discovered in the offshore region of China with confirmed natural gas geological reserves surpassing 100 billion cubic meters. However, the formation mechanism and influencing factors of shallow gas enrichment remain elusive due to the limited availability of 3D seismic and well data. This study employs seismic interpretation and digital simulation to decipher the dynamics of shallow gas accumulation and utilizes the carbon isotope composition of methane to ascertain the origin of the shallow gas. Our results show that the shallow gas is primarily concentrated within a large-scale submarine fan, covering a distribution region of up to 2800 km2, situated in the deep-sea plain. The δ13 C1 methane carbon isotope data ranges from −69.7‰ to −45.2‰ and all δ13 C2 values are above −28‰, suggesting that the shallow gas within the Ledong Formation is derived from a mix of biogenic gas produced in shallow strata and thermogenic gas generated in deeper source rocks. The results of gas sources, seismic profiles, and digital simulations suggest that thermogenic gas originating from the Lingshui and Beijiao sags was transported to the Quaternary submarine fan via a complex system that includes faults, gas chimneys, and channel sands. The mass-transported deposits (MTDs) in the upper reaches of the submarine fan have effectively acted as a seal, preventing the escape of shallow gas from the fan. Therefore, the factors contributing to the enrichment of shallow gas in the Qiongdongnan Basin include the presence of favorable submarine fan reservoirs, the availability of two distinct gas sources, the effective sealing of MTDs, and the presence of two efficient transport pathways. A conceptual model for the accumulation of shallow gas is developed, illuminating the complex formation–migration–accumulation process. This study underscores the importance of aligning multiple influencing factors in the process of shallow gas accumulation, and the suggested accumulation model may be pertinent to shallow gas exploration in other marginal sea basins.