Modern dust plays essential roles in marine sediments, providing nutrient and crucial elements for primary productivity and aquatic ecosystems. However, present marine atmospheric dust observational evidence concerning the biogeochemical response to dust deposition process is spared for a long time. Here a total of 147 aerosols samples were collected near the northern South China Sea (SCS) coast between 13 February, 2016, and 12 February, 2017, have been investigated for the grain size distribution, depositional flux, ten-day back trajectories, clusters analysis, combining with primary productivity (Chlorophyll-a concentration) to indicate the present-day dust deposition process and biogeochemical impacts in the northern SCS on the first time. Our results illustrate the deposition flux and grain size distribution change in different season, grain size distribution in winter are coarser particles than that in the summer, while the maximum and minimum dry deposition flux are 12 December, 2016, (60.4 mg m⁻² d⁻¹) and 26 August, 2016, (5 mg m⁻² d⁻¹), respective. In addition, the back trajectories and three clusters analyze results indicating 53% of air masses originating locally near the coastal areas of China from the marine boundary layer (0–0.5 km) in the summer monsoon, while 48% dust from the northeast wind is prevailing during the winter monsoon over a relatively higher level (0–1.5 km). Furthermore, an apparent Chl-a blooming after aeolian dust input with a period of 1–2 days in the SCS. Therefore, atmospheric dust contains readily bioavailable iron and enhance the biogeochemical impact in the oligotrophic SCS.