Surface sediments from the Changjiang Estuary and adjacent shelf were analyzed using a variety of bulk and molecular techniques, including grain size composition, sediment surface area (SSA), elemental composition (C, N), stable carbon isotopic composition (δ13C), n-alkanes, lignin phenols, and glycerol dialkyl glycerol tetraether lipids (GDGTs), to obtain a more comprehensive understanding of the sources and fate of sedimentary organic carbon (SOC) in this dynamic region. Bulk N/C ratios of 0.09 to 0.15, δ13C of −24.4 ‰ to −21.1 ‰, branched/isoprenoid tetraether (BIT) index of 0 to 0.74, n-alkane content of 0.02 to 0.37 mg g−1 OC and lignin content (Λ8) of 0.10 to 1.46 mg/100 mg OC and other related molecular indices in these samples indicate a mixed source of marine, soil and terrestrial plant derived OC in the study area. A three end-member mixing model using principal component analysis (PCA) factors as source markers and based on Monte-Carlo (MC) simulation was constructed to estimate the relative contributions of OC from different sources. Compared with traditional mixing models, commonly based on a few variables, this newly-developed PCA-MC model supported bulk and biomarker data and yielded a higher resolution OC inputs to different sub-regions of this system. In particular, the results showed that the average contributions of marine, soil and terrestrial OC in the study area were 35.3 %, 47.0 % and 17.6 %, and the highest contribution from each OC source was mainly observed in the shelf, inner estuary, and coastal region, respectively.