The increased atmospheric nitrogen deposition is an important part of global climate change. The study of the effects of nitrogen deposition on soil ecosystem is also attracted public attention to ecologists. Soil microorganisms, the main player in organic decomposition and nutrient cycling, play an important role in maintaining the functional diversity and sustainable development of soil. The notable increase of nitrogen deposition changes the structure and function of the soil microbial community. The different aggregate, with uneven distribution of nutrients components, provides the spatially heterogeneous microhabitat for microorganisms. In order to reveal the response of microbial community distribution on nitrogen addition in different particle size aggregates of grassland soil. Since 2010, We have set up six nitrogen addition treatments(N₀(0 kg hm^-2 a^-1), N₁₅ (15 kg hm^-2 a^-1), N₃₀ (30 kg hm^-2 a^-1), N₅₀ (50 kg hm^-2 a^-1), N₁₀₀ (100 kg hm^-2 a^-1) and N₁₅₀ (150 kg hm^-2 a^-1)) to simulate the field experiment of nitrogen deposition in Stipa baicalensis grassland in Inner Mongolia. Phospholipid fatty acid (PLFA) method was used to determine the content of microbial PLFA in three particle sizes soil aggregates (>2 mm, 0.25-2 mm and <0.25 mm diameter), to explore the effect of nitrogen addition on the microbial community structure. The results showed that the nitrogen addition increased the soil carbon and nitrogen content and decreased the soil pH. Nitrogen addition significantly increased the total PLFA content and fungal PLFA content in the microbial community of 0.25-2 mm soil aggregates. The addition of nitrogen also increased the ratio of fungal/bacterial and gram-positive bacteria/gram-negative bacteria (P<0.05) of 0.25-2 mm soil aggregates, but decreased the microbial Margalef index of soil aggregates (P<0.05). The correlation analysis showed that total PLFAs, fungi PLFAs content, the ratio of gram-positive bacteria/gram-negative bacteria and fungi/bacteria were positively correlated with soil organic carbon and total nitrogen content, but negatively correlated with C/N ratio. This study revealed that the nitrogen addition for 8 consecutive years significantly increased the soil organic carbon and total nitrogen content, decreased soil pH, and increased the fungal community of 0.25-2 mm soil aggregates, and the variation of soil organic carbon and total nitrogen was associated with the increased fungal community.