We measured particulate organic carbon (POC) fluxes from the euphotic zone into the twilight zone and deep waters (>1000 m) that occurred between the shelf and the basin in the South China Sea (SCS) and at the SouthEast Asia Time Series Station (SEATS) using floating sediment trap arrays. Additionally, selected sinking particles were imaged by scanning electron microscope (SEM) to reveal particle morphology and composition. Results showed large variations in POC fluxes with elevated values (32-104 mg-C m-2 d-1) below the euphotic zone and a trend towards lower values in the deep SCS. Vertical POC fluxes measured in deep waters between the shelf and the SCS basin were much higher than those estimated by Martin's attenuation equation. These elevated POC fluxes in deep waters were attributed to lateral particle transport as opposed to enhanced settling out of the euphotic zone. SEM images of sinking particles at 150 m show abundant marine biogenic detritus, while those in deep waters contained a higher proportion of lithogenic material. A great deal of the spatial variability in POC fluxes across the twilight zone and deep waters of the SCS cannot be represented by current biogeochemical models.