Based on a time-series sediment trap observation at a depth of 1,003-m in the northern South China Sea from 2014 to 2015, we used sinking particle flux combined with remote sensing-derived environmental data to infer the mechanisms of the biological carbon pump. Total particle flux, particulate organic carbon, CaCO 3 , and lithogenic (inorganic) fluxes peaked in winter and autumn but showed minima in summer, ranging from 59.7 to 413.2 mg m −2 d −1 , 2.1 to 18.2 mg m −2 d −1 , 32.9 to 197.9 mg m −2 d −1 , and 12.0 to 73.6 mg m −2 d −1 , respectively. Similarly, opal flux varied from 6.9 to 109.6 mg m −2 d −1 , with a prominent peak in winter and minimum in summer. However, a secondary maximum of opal in autumn was barely noticeable compared with other components. A deeper mixed-layer depth related to the northeast monsoon and surface cooling, overlapping with the effect of cyclonic eddies, is responsible for strong winter fluxes. When an anticyclonic eddy suppresses the subsurface nutrient supply, primary production and subsequent export flux in summer were reduced substantially. With respect to maximum lithogenic and CaCO 3 fluxes in autumn, a large aerosol optical depth suggests scavenging and mineral ballast effects as potential causes. This study highlights the importance of intra-seasonal physical processes (e.g., mesoscale eddies and aerosol deposition) to the deep particle flux in the South China Sea, as well as monsoonal transition.