Sedimentary organic matter (OM) in coastal systems is inherently diverse, often with multiple particulate sources and transport histories. The Taiwan Strait (TS) is a typical shallow conduit region, linking the East and South China Seas. Strong ocean currents, coastal upwellings, distal large rivers, and proximal small mountainous rivers all influence the distribution of OM in the TS. We investigated the covarying patterns in the distribution of gain size classes of sand, silt, and clay; terrestrial-sourced biomarkers (n-C_27+29+31 alkanes, n-C_26+28+30 fatty acids (FAs), and n-C_28+30+32 alkanols); marine-sourced biomarkers (phytoplankton-derived alkenones, brassicasterol, dinosterol, and zooplankton-derived cholesterol) in sea floor sediment; indicator satellite-derived primary production (Chl-a); and water-mass indicator (sea surface temperature, SST). We used an empirical orthogonal/eigen function (EOF) analysis to distinguish the influence of four hypothetical sources that entered the TS through the north, south, west, and east boundaries. Results show that input sources from the south-bound ZMCC (Zhejiang-Fujian Coastal Current) and north-bound SCSWC (South China Sea Warm Current) had the dominant influence on the OM distributions buried in the TS. Input sources via river plumes on lateral boundaries and upwellings in the TS were the secondary factors that affected the sedimentary OM distribution. Within this source-to-sink system of multiple sources and transport processes, silt and clay were the major carriers of the OM signals. Terrestrial biomarkers and primary production (Chl-a) were associated with the two major current systems and river plumes along the edge of TS. Marine biomarkers were associated with upwellings in the interior of the TS. Our finding points out that the physical systems of ocean currents, river plumes, and upwelling not only determine the distributions of biomarkers in the TS but also determine the diversity of OM in the TS.