Having differential responses to light and substrates, the vertical microorganism community structure may change correspondingly when nutrients supply from subsurface is strengthened. The bloom of algae may magnify light attenuation, consequently, the ecological structure (the niche of microorganisms) would be further changed. Thus, in the upper ocean, the kinetic processes of the light-sensitive microorganisms involved nitrogen cycle, e.g., the ammonia sink terms of oxidation and assimilation, may interconvert their dominated role. Previous ecological models embedding new and regenerated production analytical expression have been conducted. Among them, the CoSiNE model, presenting the nitrogen cycle by source and sink processes of the ammonia, nitrate and detrital nitrogen: uptake, excretion, nitrification and sinking, can reproduce the general biogeochemical features observed. However, the two stages of nitrification, ammonia oxidation and nitrite oxidation, performed by the microorganisms with different ecological traits are not included, therefore, the vertical distribution of nitrite with nanomole magnitude was missed. In this study, we upgrade the the CoSiNE ecological model with sophisticated nitrification process in the upper ocean and validate the model with field observed and experimental data, trying to bridge the gap of simulated results and realistic mechanism. On this basis, we aim to discuss the fluctuation of new and regenerated production under the biological-physical multiple effects.