To understand the driving mechanism of nitrogen deposition on greenhouse gases-emission from forest soil, we studied soil physical and chemical properties, microbial community structure and greenhouse gas-emission of potted soil of two-years old Pinus massoniana, fertilized with nitrogen. The results showed that simulated nitrogen deposition treatment significantly increased soil available nitrogen and seedling root nitrogen level. Soil microbial carbon (SMBC) decreased by 78% compared with that of the control. In contrast, soil microbial nitrogen (SMBN) increased by 2.6 times from that of control. Simulated nitrogen deposition treatment significantly reduced the level of soil total microbials. Nitrogen application had a significant effect on the soil emission rates of N₂O and CO₂:the N₂O emission rate increased with higher level of nitrogen application, the CO₂ emission rate also increased in the short term but decreased at the later stage due to the significant decrease of soil microbials. Correlation analysis showed that soil pH, temperature, moisture, available nitrogen, SMBN and SMBC were all ralated to CO₂ and N₂O emission rates. Step-wise regression analysis showed that the amount of nitrate N was the dominant factor affecting soil CO₂ and N₂O flux. Larger amount of root in the soil from the three-plant pots was beneficial to absorb and reduce the excessive nitrogen in soil and decrease N₂O emission. In conclusion, our study illustrated the effects of nitrogen deposition or excessive N fertilization on soil nitrogen content, soil pH, root biomass and soil microbial community structure and other variables, which directly or indirectly affect the emission rate of soil greenhouse gas. Soil nitrate accumlation caused by N deposition or N fertilization or N fertilization is conductive to accelerating soil greenhouse gases (CO₂ and N₂O) emission.