Burial of terrestrial organic carbon (OCterr) in marginal sea sediments is a key component of the carbon cycle, exerting long-term influence on atmospheric CO2 and climate. Assessment of the burial efficiency of OCterr is of key importance, yet remains poorly constrained due to current gaps in our knowledge of mechanistic controls, including the influence of organic matter composition and age on the fate of OCterr in marine sediments. We measured bulk characteristics (δ13C and Δ14C of OC; mineral surface area, SA; grain size; n = 98 samples) and biomarker carbon isotopic compositions (fatty acid δ13C and Δ14C; n = 11) of a suite of surface sediment samples from the Bohai Sea and Yellow Sea (BS-YS). Combining with published results, bulk OC (n = 234) and biomarker (n = 19) carbon isotopic data are used to examine spatial variability in the sources and ages of OCterr in this shallow marginal sea system. Biomarker carbon isotopic values are used to constrain endmember values, and a dual carbon isotope mixing model was applied to all bulk samples to develop a spatially explicit assessment of contributions of different pools of OCterr. Although highly spatially variable, pre-aged OC (OCpre-aged) and fossil OC (OCfossil) when combined (i.e., “non-modern OC”) on average accounted for 51 ± 10% of the OC in BS-YS surface sediments. This was equivalent to the proportion of OCterr (ave., 51 ± 14%) estimated from a δ13COC binary mixing model, suggesting OCterr in the mixed layer of BS-YS sediments is predominantly composed of millennial-aged OC. The burial potential of pool-specific OCterr was then evaluated through comparison of corresponding mineral SA-normalized loadings of surface sediments with those of Yellow River suspended particulate matter. Both the regression slope and the arithmetic mean value approaches reveal high burial potential for all terrestrial OC pools delivered by Yellow River, which is attributed to the aged and refractory nature of OC exported from the Yellow River. However, differing relationships of pool-specific OCterr loadings between BS-YS and Yellow River sediments imply contrasting fates. In particular, we find that the burial potential of OCpre-aged is consistently greater than that of OCfossil. This surprising observation suggests either enhanced degradation of OCfossil during lateral transport (possibly as a consequence of different mineral associations and hydrodynamic sorting effects), or additional sources for OCpre-aged, such as from small rivers or aerosol deposition. Overall, OC age, mineralogical composition and hydrological settings contribute to the complex patterns of OC residing in northern China marginal sea surface sediments. This novel molecular-isotopic approach reveals significant spatial variability in proportions, contents and burial potential among terrestrial OC pools, and underlines the importance of considering organic matter age and composition in understanding and constraining the fate of OCterr in marine sedimentary environments.