In order to study the effect of nitrogen fertilizer and its distribution with organic fertilizer on microbial residual nitrogen accumulation and distribution in aggregates in agricultural soils, this study was conducted in Shaya County, Aksu Region, southern Xinjiang, for three consecutive years in a field location experiment, setting up a total of 10 treatments with five nitrogen fertilizer application levels (0, 200, 300, 400, and 500 kg/hm₂^{) and cattle manure (3000 kg/hm₂}) on top of these five nitrogen application levels, to analyze the distribution of agglomerates at different treatments in grain size and their N content of fungal and bacterial residues were analyzed under different treatments. The results showed that: single application of nitrogen fertilizer could increase the proportion of large and small agglomerates and decrease the proportion of micro agglomerates and powdery sticky grains; different amounts of nitrogen fertilizer with cattle manure could increase the proportion of large agglomerates and decrease the proportion of small agglomerates. The same amount of nitrogen application with cattle manure could only significantly increase the total nitrogen content in the powder and sticky grains. The proportion of microbial residue nitrogen content to total nitrogen content ranged from 29.48% to 37.77%, and the proportion of fungal and bacterial residue nitrogen content to microbial residue nitrogen content ranged from 65.57% to 75.83% and 26.48% to 35.69%, respectively. The application of nitrogen fertilizer could increase the content of microbial residual nitrogen, especially the fungal residual carbon; when the application of nitrogen was higher, the dosing of cattle manure increased the content of microbial residual nitrogen from bacteria. Both nitrogen only and nitrogen fertilizer with cattle manure decreased the fungal residual nitrogen content in large and small aggregates and microaggregates, but increased the bacterial residual nitrogen content. The following conclusions were drawn: application of nitrogen fertilizer and its combination with cattle manure altered the distribution of aggregates and increased the total and microbial residual nitrogen content of the soil; and the combination of cattle manure contributed to the accumulation of microbial residual nitrogen at higher nitrogen application rates.