The Pearl River plays an important role in transporting terrestrial organic carbon (OC) to the South China Sea (SCS). However, the sources and compositional distribution of OC in the system are poorly understood. This study focused on delineating the sources and determining the fate of surface sedimentary OC from the Feilaixia Hydropower Station to the coastal SCS. Elemental, stable carbon/nitrogen isotope (δ13C and δ15N), and lignin‐phenol analyses have been conducted. The total OC (TOC) from the upstream sites were generally derived from vascular plants (higher C/N and and depleted δ13C) and soils. Additional input was attributed to riverine primary production (lower C/N and enriched δ13C), which was enhanced near the dam‐created reservoir. The C/N and δ13C values were not significantly different among sites in the midstream. The estuary/coastal sites witnessed hydrodynamically sorted riverine OC, which was diluted by marine primary production (lower C/N and more enriched δ13C). The lignin concentration was the highest in the upstream sites, remained relatively unchanged in the midstream sites, and decreased significantly along the estuary/coastal sites, which was corroborated by variation in TOC. A comprehensive five‐end‐member Monte Carlo simulation suggested that previous studies had underestimated the C4 plant input by 14 ± 11% and overestimated the riverbank soil input by 21 ± 17%. Thus, our study provided valuable information for more accurate source and mass balance studies of terrestrial OC transported to the SCS, which helped to further understand the carbon cycling in the large river‐ocean continuum.