The rapid economic developments in countries surrounding the South China Sea have caused a significant increase in the atmospheric deposition of nitrogen (AD‐N) into the ocean. The impact of AD‐N on the regional ecosystem has not been quantitatively assessed, and its driving mechanism has not been explored, either. Here, we applied a one‐dimensional European Regional Seas Ecosystem Model to examine the responses of the ecosystem to AD‐N. The physical‐biological coupled model reproduced the seasonal and interannual variabilities of observed nutrients, chlorophyll a, phytoplankton community structure, and particulate organic carbon (POC) exports at the South East Asia Time‐series Station. Seasonally, the increase of POC flux by AD‐N was most significant in winter, with a ∼2‐month lag behind the associated surface response. It can exist in the following spring, as supported by the larger population size of zooplankton after the previous winter's feeding up. Notably, the ratio of POC export to primary production varied seasonally and interannually, which was controlled by the phytoplankton and zooplankton's size compositions. The surface nutrient input thus caused a significant seasonal change in the biological carbon pump efficiency. Interannually, the modulation of the POC flux by AD‐N was inversely phase‐locked with wind variations. The out‐of‐phase of the surface‐ and subsurface‐nutrient‐driven POC fluxes suggested a potentially more considerable contribution of AD‐N to the total carbon export during years under the weak subsurface influence. This study highlights the importance of AD‐N in the regional ecosystem, which needs a better representation in the present biogeochemical modeling framework.