The sensitivity of ocean phytoplankton (chlorophyll-a concentration) to deposition of atmospheric inorganic nitrogen compounds over Japan Sea was investigated using a 3-D lower trophic-marine ecosystem model (COCO-NEMURO) combined with an atmospheric regional chemical transport model (WRF-CMAQ). The monthly mean values for the wet and dry deposition of inorganic nitrogen compounds including gases (HNO3 and NH3) and aerosol particles (NO3－ and NH4＋) over the Japan Sea were determined using the WRF-CMAQ. The results indicated that the total flux of inorganic nitrogen compounds was in the range of 82–302 μmol/m2/day and wet deposition was dominant in all season. These values were input into the ocean surface in NEMURO as a new nitrogen nutrient source from atmosphere. The annual average of surface chlorophyll-a concentration over Japan Sea was increased from 0.26 to 0.35 mg/m3. The chlorophyll-a concentration in summer season was ~2.1, while that in winter season was ~1.1, times higher than that without atmospheric inorganic nitrogen compounds deposition, indicating that the atmospheric deposition of inorganic nitrogen compounds significantly influence surface chlorophyll-a concentration in summer season.