Anthropogenic nitrogen (N) deposition and increased precipitation are known to alter soil microbial communities. However, the interactions between N deposition and increased precipitation on soil microbial composition and the microbial-mediated carbon (C) and N cycling functions remain unclear. A 10-year experiment was conducted on the Mongolian Plateau to evaluate the effects of N deposition (0, 10 g N m⁻² year⁻¹) and water addition (0%, 30% above average annual precipitation) on: (1) soil nutrient dynamics and pH, and (2) their subsequent impacts on bacterial community structure and C/N cycling functions. We found that long-term N deposition significantly altered the bacterial community composition, specifically increased the abundance of Alphaproteobacteria, Firmicutes, and Bacteroidetes while reducing Acidobacteria. It also simplified bacterial network complexity and stimulated C metabolic functions (aromatic compound degradation, cellulolysis, hydrocarbon degradation). Water addition enhanced functions linked to chitin degradation, aromatic compound degradation and nitrogen fixation. Structural equation modeling suggests N deposition indirectly promoted C cycling via soil acidification, while water addition directly boosted N cycling and indirectly influenced it through soil organic carbon. Our findings underscore that N deposition will enhance bacterial C acquisition and emphasize the importance of pH in regulating microbial nutrient cycles. This study provides new experimental insights into the potential mechanisms by which nutrient inputs and precipitation changes affect microbial community structure and functions of the C and N cycling.