Abstract: In the Pearl River Mouth Basin of the northern South China Sea, extensive commercial shallow gas reservoirs have recently been discovered. However, their formation mechanisms remain poorly constrained. This study employs integrated petroleum geological and geochemical datasets to elucidate shallow gas systems' genesis and geochemical signatures. Key findings demonstrate that shallow gas reservoirs exhibit distinct geochemical differentiation from deep thermogenic counterparts, characterized by elevated dryness coefficients (> 0.9), depleted methane δ13C values (−52‰ to −34.4‰), and 13C-enriched ethane and propane isotopes resulting from migration fractionation. The anaerobic environment minimizes microbial alteration, while the complex marine geology challenges conventional interpretations of isotopic source indicators. Light hydrocarbon analysis identifies type II2-III kerogen as the primary thermogenic gas source, with southern reservoirs showing sapropelic organic matter signatures consistent with oil-cracking origins. Notably, mixed-source reservoirs display an inverse δ13C relationship between carbon dioxide and methane, contrasting with positive correlations typically observed in biogenic gas from carbon dioxide reduction. Quantitative end-member modeling constrains biogenic contributions to ≤ 30%, confirming thermogenic dominance despite active methanogenesis. Shallow gas accumulation is a dynamic process involving simultaneous charge and diffusion. Synthesizing these insights with prior research, we propose a genetic model for shallow gas reservoirs, highlighting significant differences in source rock maturity, kerogen types, enrichment layers, migration channels, and water depths relative to deep-water counterparts.