Submarine gas hydrate systems store vast carbon inventories (∼1500–12,400 Gt C) yet pose dual risks as potential geohazard multipliers and climate feedback agents under oceanic warming. Conventional seal assessment fails catastrophically in unconsolidated Quaternary hydrate-bearing sediments due to core-retrieval artifacts, hydrate morphology controls on capillary trapping, and meter-scale heterogeneity unresolved by seismic methods. Here, we pioneer methane carbon isotope (δ13C1) gradients as a dynamic proxy for seal capacity in the Qiongdongnan Basin. Integrating petrographic features, natural gas geochemical characteristics, downhole logging data, and principal component analysis (PCA) from six wells, we: (1) quantified the thermogenic gas contribution of wells W6 and W8 to be 55%–73%, and that of well W1 to be 28%–32% via binary mixing models, (2) establish that methane carbon isotope gradients >0.5‰/m diagnose effective capillary barriers, correlating with zones of pore-throat disconnection, and (3) develop a PCA-integrated logging model (cumulative variance: 84.02%, R2 = 0.78) predicting seal capacity from conventional petrophysical parameters. Furthermore, the results validate a charge-dynamic barrier-mixing accumulation model where thermogenic gas influx elevates hydrate saturation, creating self-sealing horizons that trap underlying microbial gases and subsequently charged thermogenic gases, recorded in diagnostic methane carbon isotope reversals. This approach bridges molecular-scale fractionation and reservoir-scale processes, enabling targeted identification of high-integrity seals for optimized carbon storage and safer hydrate exploitation in rapidly deposited marginal basins.