Warming and nitrogen (N) deposition are two major global change factors that co-occur and profoundly affect terrestrial ecosystem structure and function. Arid ecosystems, which are characterized by water and nutrient limitation, are particularly sensitive to global change. Soil microorganisms are the key drivers of soil carbon (C) cycling, mediating the decomposition of soil organic carbon (SOC) and the formation of microbial biomass carbon (MBC). However, the interactive effects of warming and N deposition on soil microbial functional traits and their regulatory mechanisms on C cycling in arid ecosystems remain unclear. This study conducted a 4-year in-situ interactive experiment of warming and N deposition in the Tengger Desert (a typical arid ecosystem in Northwest China), with four treatments: control (CK), warming (W), N deposition (N), and warming + N deposition (W+N). The effects of these treatments on soil microbial community composition, functional enzyme activities, functional gene abundances related to C cycling, and SOC fractions were investigated using high-throughput sequencing, extracellular enzyme activity assay, and quantitative real-time PCR (qPCR). The results showed that warming and N deposition had significant interactive effects on soil microbial communities and C cycling processes. Compared with CK, W treatment significantly reduced microbial alpha diversity (Shannon index decreased by 18.3%) and MBC content (decreased by 22.5%), while N treatment significantly increased these indices (Shannon index increased by 12.6%, MBC increased by 15.8%) (P < 0.05). The W+N treatment alleviated the negative effects of warming on microbial diversity and MBC (Shannon index and MBC were not significantly different from CK). At the community level, warming promoted the enrichment of drought-tolerant taxa (e.g., Actinobacteria, Ascomycota), while N deposition favored copiotrophic taxa (e.g., Proteobacteria, Basidiomycota). The interactive treatment (W+N) formed a unique microbial community dominated by both drought-tolerant and copiotrophic taxa. Functionally, warming significantly inhibited the activities of C-degrading enzymes (β-glucosidase, cellulase, and lignin peroxidase) and the abundance of corresponding functional genes (cbhI, lcc), while N deposition enhanced them. The W+N treatment significantly increased enzyme activities and functional gene abundances compared with W treatment (β-glucosidase activity increased by 35.2%, cbhI gene abundance increased by 42.6%) (P < 0.05). Redundancy analysis (RDA) and structural equation modeling (SEM) showed that soil temperature, moisture, and available N (AN) were the key environmental factors driving microbial community and functional changes. The interactive effect of warming and N deposition regulated soil C cycling mainly by altering microbial functional enzyme activities and functional gene abundances. This study reveals the interactive regulatory mechanisms of warming and N deposition on soil microbial functions and C cycling in arid ecosystems, providing an important theoretical basis for predicting the response of arid ecosystem C balance to future global change.