River-dominated ocean margins represent one of the most significant carbon sink centers in the ocean. However, the mechanisms governing organic carbon (OC) burial under the influence of complex sedimentary processes in estuarine regions remain poorly understood. In this study, we analyzed sediment core YE12-24L and sub-core YE12-24S collected from the Yangtze River estuary, utilizing multiple proxies including grain size, relative elemental contents, total organic carbon (TOC), ²¹⁰Pb dating, and lignin biomarkers. Our results reveal three distinct deposition units formed under varying depositional regimes. Deposition Unit 1 (DU1), composed of fine-grained sediments primarily derived from riverine suspended matter, underwent cycles of resuspension and redeposition prior to burial; the OC burial efficiency in this unit was predominantly governed by the duration of pre-burial resuspension. Deposition Unit 2 (DU2) originated from rapid flood-induced deposits, within which approximately 12% of the OC was degraded during early diagenesis. Deposition Unit 3 (DU3) was attributed to typhoon-induced deposits, involving transport, resuspension, and differential settling. Notably, about 83% of the OC in DU3 was degraded during early diagenesis, with this degraded fraction consisting predominantly of young, marine-derived OC. Collectively, these findings contribute to a deeper understanding of OC burial mechanisms under complex environmental forcing and provide critical insights for quantifying the impact of early diagenesis on OC burial in large river estuaries.