Microorganisms govern soil nutrient cycling. It is therefore critical to understand their responses to human-induced increases in N and P inputs. We investigated microbial community composition, biomass, functional gene abundance, and enzyme activities in response to 10-year N and P addition in a primary tropical montane forest, and we explored the drivers behind these effects. Fungi were more sensitive to nutrient addition than bacteria, and the fungal community shift was mainly driven by P availability. N addition aggravated P limitation, to which microbes responded by increasing the abundance of P cycling functional genes and phosphatase activity. In contrast, P addition alleviated P deficiency, and thus P cycling functional gene abundance and phosphatase activity decreased. The shift of microbial community composition, changes in functional genes involved in P cycling, and phosphatase activity were mainly driven by P addition, which also induced the alteration of soil stoichiometry (C/P and N/P). Eliminating P deficiency through fertilization accelerated C cycling by increasing the activity of C degradation enzymes. The abundances of C and P functional genes were positively correlated, indicating the intensive coupling of C and P cycling in P-limited forest soil. In summary, a long-term fertilization experiment demonstrated that soil microorganisms could adapt to induced environmental changes in soil nutrient stoichiometry, not only through shifts of microbial community composition and functional gene abundances, but also through the regulation of enzyme production. The response of the microbial community to N and P imbalance and effects of the microbial community on soil nutrient cycling should be incorporated into the ecosystem biogeochemical model.