With the intensification of human activities, nitrogen (N) deposition has become a major global change factor affecting terrestrial ecosystem structure and function. Arid zone ecosystems are inherently N-limited, making them highly sensitive to exogenous N input. Soil microorganisms are the core drivers of soil N cycling processes, but the mechanisms by which N deposition regulates microbial community structure and further affects N transformation in arid zones remain unclear. This study conducted a 3-year in-situ N deposition simulation experiment in the southern Gobi Desert (a typical arid zone in Northwest China) to explore the effects of different N deposition levels (control, low N, medium N, and high N) on soil bacterial and fungal communities, as well as key N cycling functional processes. High-throughput sequencing, functional gene quantification, and soil N fraction determination showed that N deposition significantly altered microbial community composition, diversity, and co-occurrence network structure. Compared with the control, medium and high N deposition significantly reduced bacterial alpha diversity (Shannon index decreased by 15.7% and 23.2%, respectively) but increased fungal alpha diversity (Shannon index increased by 11.3% and 18.5%, respectively). The microbial co-occurrence network under high N deposition showed lower complexity (node number decreased by 42.1%) and stability (modularity decreased by 28.6%) than the control. Taxonomically, N deposition promoted the enrichment of copiotrophic taxa (e.g., Proteobacteria, Ascomycota) and inhibited oligotrophic taxa (e.g., Actinobacteria, Basidiomycota). Functionally, low and medium N deposition enhanced the abundance of functional genes related to nitrification (amoA) and denitrification (nirK, nirS), while high N deposition significantly inhibited these genes and increased the abundance of N fixation genes (nifH). Redundancy analysis revealed that soil pH, available N (AN), and electrical conductivity (EC) were the key drivers of microbial community changes. Structural equation modeling indicated that N deposition regulated arid zone soil N cycling mainly by altering microbial community composition and functional gene abundance. This study clarifies the response patterns and functional consequences of soil microbial communities to N deposition in arid zones, providing a theoretical basis for predicting the dynamics of arid zone ecosystems under future global change scenarios.