In the temperate to tropical forested ecosystems, many studies have traditionally been conducted with focusing on the effects of excess N depositions on ecosystem functions, including several model developments. Many of those are lumped style models expressing the net rate of transformations and flows of N, and are not sufficiently model the mechanisms, such as microbial activities behind the biogeochemical appearance of N transformation. The aim of our model is to analyze the processes through three nitrogen stocks (organic N, NH4+-N, NO3--N) but also the integration (link) with the plant growth and carbon cycle in the forest environmental conditions. The relevant part of this model implementation is: 1) Nitrogen cycle in the soil; 2) Plant biomass dynamics; 3) Carbon cycle in the soil, and including daily precipitation and potential evapotranspiration. Nitrogen transformation in this model is expressed conceptually by the microbial activities, which is regulated by the carbon resources and environmental parameters, such as temperature and moisture conditions. We tested the model performance on the long-term (monthly time steps, few 100 years’ scale) simulation with considering the plant growth. We confirmed that the model could successfully simulate the long-term trend of the biomass growth and nitrogen storages of each form, and responses against the nitrogen deposition increase. We discuss the mechanisms behind the linkage between carbon and nitrogen availabilities in soil in relation to the progress of the nitrogen saturation under excess atmospheric nitrogen input.