In order to study the effects of nitrogen fertilizer and its combined application with organic fertilizer on the occurrence and distribution of microbial residual nitrogen in aggregates in farmland soils in arid areas, a field positioning test was carried out in Shaya County, Aksu Prefecture, southern Xinjiang. A total of 10 treatments were set up with 5 nitrogen application rates (0, 200, 300, 400, 500 kg/hm²) and 5 nitrogen application rates combined with cattle manure (3 000 kg/hm²). In the third year of the experiment, the particle size distribution of soil aggregates, the contents of fungal and bacterial residue nitrogen were determined at the boll opening stage of cotton. The results showed that, single application of nitrogen fertilizer increased the proportion of large and small aggregates and decreased the proportion of micro aggregates, silts and clays; different amounts of nitrogen fertilizer with cattle manure increased the proportion of large aggregates and decreased the proportion of small aggregates. The same amount of nitrogen application with cattle manure only significantly increased the total nitrogen content in silts and clays. The proportion of microbial residue nitrogen content to total nitrogen content ranged from 35.93% to 49.81%, and the proportion of fungal and bacterial residue nitrogen contents to microbial residue nitrogen content ranged from 65.57% to 75.83% and 26.48% to 35.69%, respectively. The application of nitrogen fertilizer increased the content of microbial residual nitrogen, especially the fungal residual nitrogen; 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 fungal residual nitrogen content in large and small aggregates and microaggregates, but increased bacterial residual nitrogen content. In conclusion, the application of nitrogen fertilizer and its combination with cattle manure altered the distribution of aggregates and increased the total and microbial residual nitrogen content in soil; and the combination of cattle manure contributed to the accumulation of microbial residual nitrogen at higher nitrogen application rates.