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Enhanced atmospheric nitrogen deposition can greatly influence the soil nitrogen content and soil microorganisms in terrestrial ecosystems. However, there is a lack of knowledge about the response of soil microbes to changes in soil nitrogen, particularly in desert ecosystems. To address this, we used long-term artificial nitrogen addition to simulate atmospheric nitrogen deposition in a desert ecosystem in Ningxia, China. We adopted a high-throughput sequencing method (16S rRNA and ITS) to explore the effects of different amounts of atmospheric nitrogen deposition on soil microbial diversity and community structure. Six years of nitrogen addition (6 g N m−2 y−1) significantly increased the soil organic carbon content and the total soil nitrogen content (p 0.05). Further analysis revealed that nitrogen addition substantially reduced the number of positive correlations between soil microbial species and the number of core microbial species. Our results suggest that for desert ecosystems, at present, atmospheric nitrogen deposition may increase soil nitrogen use by some vegetation but it does not alleviate the competition for soil nitrogen between soil microbes and vegetation. Moreover, although enhanced atmospheric nitrogen deposition did not significantly change the soil microbial community structure, it may negatively affect the interactions among soil microbial species. This would hinder soil microbial adaptation to the changing environment and the development of desert ecosystems.