As one of the main interfaces of the Earth system, estuaries show the strongest land–sea interaction in the carbon cycle, which links terrestrial ecosystems to the marginal sea. Furthermore, estuaries are considered as one of the most active intermediate reservoirs for both terrestrial and marine matter due to complex hydrodynamic processes regulated by the river runoff, wave and tide. Processing of organic matter (OM) in tidal estuaries modifies its transfer and transformation from the river to the sea, so studies of on the source and distributions of estuarine OM can help us understand the behavior of production, exchange, transport and burial of diverse OM within this transition zone before entering the marginal sea. In this paper, we took the Minjiang River Estuary (MRE) as a typical system in which there is strong influence of the tide. The source, composition and spatial distribution of OM in surface sediments of MRE were deciphered based on multiple organic geochemical properties for source-specific biomarkers (n-alkanes, n-alkanols, sterols) and bulk OM. Results show that sedimentary organic components were negatively correlated with sediment grain size, which indicates fine particles such as silt and clay are the major carriers of the OM signals in tidal estuaries. Source-specific biomarker proxies indicate that in terms of source diversity the sedimentary OM in the MRE shows mixed signals of terrestrial and marine sources, and the proportion of terrestrial OM decreases with the increase in distance from the land. The fractional contributions of OM from the riverine (i.e., terrestrial), marine and deltaic sources were quantitatively estimated using a Monte Carlo (MC) three-end-member mixing model based on C/N and δ13C values, and the average contributions of the three sources are 40 ± 10%, 48 ± 10% and 12 ± 4%, respectively, with little contribution from deltaic sources. The dispersion of sedimentary OM from different sources in the MRE is primarily controlled by the depositional environment determined by dynamic conditions and tidal processes play a significant role in the redistribution of sedimentary OM dispersion patterns. Compared with other large estuaries in southeast China, the OM accumulation contribution in the tide dominated small and medium-sized estuaries such as the MRE which is largely dependent on riverine and marine deliveries. The MRE has a high potential for both terrestrial and marine organic carbon (OC) burial, with an accumulation rate of 3.39 ± 1.83 mg cm−2 yr−1 for terrestrial OC, and an accumulation rate of 3.18 ± 0.68 mg cm−2 yr−1 for marine OC in muddy sediment, making it an important contributor to the sedimentary carbon sink of the marginal sea.