Large river‐dominated margins play a potential key role in regulating global carbon cycle and budget due to high terrestrial organic carbon (Corg) inputs and sediment accumulation rates. Here bulk elements (Corg and TN), isotopic compositions (δ13Corg and δ15N), radioisotope 210Pb, sedimentary grain size, pH, Eh, and physicochemical properties were analyzed on samples from the Yangtze River Estuary to determine the mechanism involved in transporting sedimentary Corg offshore. In addition, nine box‐cores were analyzed to further reveal the potential effects of the declining sediment load on the modern depositional pattern of Corg. The statistical analyses indicate that the hydrodynamically driven sediment composition exerts a significant control on the transport, mobilization, and accumulation of sedimentary Corg from the river to the estuary, with respect to the redistribution of fine‐grained sediments. Furthermore, X‐radiographs and 210Pb indicate that reworked environment dominates carbon burial in the Yangtze proximal deposit, while a stable sedimentary environment of Corg (3.50–5.58 g cm−2 year−1) is observed in the Yangtze distal mud. Notably, the enhanced erosional inputs that contain terrestrial plant debris (mainly the coarse fractions) have tended to become important sources for Corg. Although reworked sediments in the Yangtze River Estuary are frequently exposed to oxygen during physical and biological processes, there appears to be a high potential for long‐term sedimentary Corg storage, due to its association with sediment particles (mainly the clay fractions) that provide physical protection against its degradation.