The burial of sediment organic matter (SOM) in the estuary and shelf plays an important role in the global carbon cycle. However, it is challenging to determine the source, composition, and burial of SOM in the coastal sea, especially at the molecular level. This was explored in the coastal area outside the largest Yangtze River of China with multiple techniques including elemental and stable isotopic analysis, absorption spectroscopy, fluorescence excitation-emission matrices coupled with parallel factor analysis (EEMs-PARAFAC), and ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). The end-member mixing analysis based on δ13C and δ15N showed a dominance of marine contribution (up to 70%) at most stations while the terrestrial contribution increased to >55% nearshore in summer at a high fluvial sediment flux. This was consistent with the offshore decreasing humic-like C1 and C2, humification index (HIX), %lignin-like compounds, and %CHO but increasing tryptophan-like C3, biological index (BIX), %protein-like compounds, and %CHOS from EEMs-PARAFAC and FT-ICR-MS analysis. The %clay correlated positively with SOM content, HIX, %lignin-like compounds, O/C, and modified aromaticity index (AImod) but correlated negatively with %C3, H/C, and the relative abundance of labile formulas (MLBL), while %silt showed contrasting correlations. These results indicated the fine clay sediments adsorbed more humified, aromatic, oxygenated, and terrestrial compounds that were probably more resistant to biodegradation and thus had a higher burial efficiency than those on the silty sediments. Principal component analysis based on SOM indices further revealed different characteristics of SOM in the nearshore, northern offshore, and southern offshore regions, which were probably dependent on the delivery by local current systems. Overall, these findings contributed to unraveling the source and molecular composition of SOM associated with different grain size sediments and local current delivery, which are fundamental for understanding the factors underlying carbon burial in the complex coastal environment.