Abstract The impact of atmospheric deposition on deep‐ocean carbon export in the subtropical Northwest Pacific remains poorly evaluated. Using sediment trap data and a newly improved biogeochemical model, we show that iron deposition in winter and spring and nitrogen deposition in summer and fall are important drivers for the seasonal variability of deep‐ocean particulate organic carbon (POC) export flux. Nitrogen deposition can stimulate pico‐plankton growth in summer and fall, which leads to increases of microzooplankton and mesozooplankton. The increase of mesozooplankton exerts higher grazing pressure on diatoms in winter and early spring, which then reduces deep‐ocean POC export due to the reduction of ballasting mineral of opal. Iron deposition only affects the region in winter and spring when nitrogen is not a limiting factor for phytoplankton growth; and it can increase deep‐ocean POC export by stimulating diatom growth and opal production.