Iron-mediated preservation of organic carbon (OC) is an important pathway for carbon burial in estuarine and coastal sediments, yet whether this process operates similarly across organic carbon sources remains poorly constrained. Here, we investigated source-specific Fe-mediated organic carbon preservation in surface sediments from the Pearl River Estuary and adjacent coastal region by combining sequential water and HCl extraction, bulk OC and Fe measurements, δ¹³C and C/N-based source apportionment, Δ¹⁴C analysis, optical indices, and FT-ICR MS molecular characterization. HCl extracted more OC and Fe than water (6.2 ± 0.7% of bulk sediment OC and 101.3 ± 35.1 μmol Fe g⁻¹ for HCl extract, versus 4.8 ± 0.7% and 0.17 ± 0.16 μmol Fe g⁻¹ for water extract). At the molecular level, acid-extractable organic matter was enriched in higher-mass, oxygen-rich, aromatic, oxidized, and CRAM-like formulas, indicative of compositionally mature organic matter. Molecular formulas of iron-associated OC (FeOC-MFs) differed by source. Terrestrial and riverine primary production-associated FeOC-MFs were negatively correlated with OC/Fe and had aromatic, oxygen-rich, unsaturated, and oxidized signatures, whereas marine-associated FeOC-MFs were positively correlated with OC/Fe and were more H-rich and heteroatom-enriched. The formula-weighted average atomic composition was distinctly different for the three sources, being C_15.7H_12.3O_7.59N_0.16 for terrestrial-associated FeOC-MFs, C_22.7H_17.0O_13.5N_0.20 for riverine primary production-associated FeOC-MFs, and C_13.2H_18.0O_6.70N_1.45S_0.12P_0.08 for marine-associated FeOC-MFs. Together, these results advance Fe-mediated organic matter preservation from a bulk mineral-association concept to a source-resolved molecular framework, showing that OC from different sources may be selectively stabilized through distinct Fe-OC associations during land-to-sea transport.