Increasing nitrogen (N) deposition severely impacts terrestrial biogeochemical cycles by altering the stoichiometry of ecological components. Although microbes are known to play an important role in biogeochemical cycles, the mechanisms how soil microbes drive nutrient cycling remain elusive under N deposition. Therefore, we investigated changes in microbial community diversity, composition, and interactions, and elucidated the relationship among microbial community responses, soil available nutrients, and ecological stoichiometry resulting from two years of N addition to a Pinus tabuliformis plantation on the Loess Plateau at four rates of N addition (0 (N0), 3.0 (N3), 6.0 (N6), and 9.0 (N9) g N m−2 y−1). N addition significantly influenced microbial composition, decreasing the relative abundance of Acidobacteria and Basidiomycota along N addition gradients and increasing the relative abundance of Ascomycota from N3 to N9. Along N addition gradients except N3, bacterial interactions increased from 62.70% to 73.38%, whereas interactions between bacterial and fungal communities decreased from 34.44% to 24.43%. Among all microbial interactions, the positive ones accounted for a larger proportion (over 55%), indicating a predominance of mutualism under all N addition treatments. Changes in the microbial composition were correlated with soil resource stoichiometry factors, including soil organic carbon: soil total N (SOC:TN) and SOC: soil total phosphorus (SOC:TP), whereas the topological network features were correlated with ammonium N (NH4+-N), nitrate N (NO3−-N), β-1,4-N-acetylglucosaminidase (NAG), alkaline phosphatase (AP), and eco-enzymatic stoichiometry. Therefore, the soil variables that caused changes to microbial composition and interactions were different. In this sense, microbial community compositions were more easily affected by soil resource stoichiometry, whereas microbial interactions were more easily affected by soil available nutrients. In addition, changes to microbial interactions could mediate microbial metabolism via eco-enzyme expression.