The increasing atmospheric nitrogen deposition has a profound impact on soil nutrient cycling processes, and the soil enzyme is a key regulatory pathway. Due to the differences in soil aggregate structure and environment, the nutrient transformation processes mediated by enzyme activities may be different in soil aggregates of different sizes. However, the response of nutrient transformation-related enzyme activities to nitrogen deposition in soil aggregates in semi-arid areas is still unclear. This study was based on a 3-year field experiment of nitrogen addition on natural grassland on the Loess Plateau. The soil basal physicochemical properties, nitrogen (L-leucine aminopeptidase, LAP and β-1, 4-N-acetylglucosaminidase, NAG) and phosphorus (phosphomonolipase, PME, phosphodiesterase, PDE, and phytase, phyA) transformation-related enzyme activities and enzyme stoichiometry ratios in different sized soil aggregates under different levels of nitrogen addition were analyzed to explore the effect of nitrogen addition on the enzyme activities of the aggregates. The results showed that (1) the nitrogen addition led to a significant decrease of pH in different soil aggregates, and high nitrogen addition levels caused a significant increase in soil organic carbon, total N, nitrate N, C:P and N:P in all soil aggregates. (2) The soil PME, PDE and phyA activities in different sized aggregates decreased and then increased, while the soil LAP, NAG activities, and enzyme N:P ratio increased with the increasing levels of nitrogen addition. The order of enzyme activities in soil aggregates was small aggregates (<0.25 mm)>medium aggregates (0.25-2 mm)>large aggregates (>2 mm). (3) Nitrogen addition regulated soil enzyme activities related to P transformation by affecting soil N nutrients in medium and large aggregates. In conclusion, nitrogen addition affected the enzyme activities related to N and P transformation by changing soil nutrients and their stoichiometric ratio and pH in soil aggregates.