Root and leaf litters are two important litter sources in ecosystems, providing carbon sources and nutrients for microorganisms. The decompositions of root and leaf litters are highly sensitive to the environmental availability of nutrients. The simultaneous deposition of nitrogen and phosphorus is one of the most critical challenges in ecosystems worldwide. Changes of nitrogen and phosphorus inputs can affect both the decomposition rates of root and leaf litter and other responses of the ecosystem. The long-term patterns of mass loss during leaf and root litter decomposition are well documented, but the responses of microbial community structure and enzyme activity in root and leaf debris to the simultaneous deposition of exogenous nitrogen and phosphorus are not known. Understanding the influence of simultaneous inputs of exogenous nitrogen and phosphorus on the microbial community structure and enzyme activity in root and leaf debris can help us to precisely predict shifts in ecosystem processes in nitrogen and phosphorus deposition enriched regions. We investigated the responses of microbial community structure (cyclopropyl fatty acids/precursor structure, Cy/pre; monounsaturated fatty acids/saturated fatty acid, Mono/sat; fungus/bacteria, F/B; Gram-positive bacteria/Gram-negative bacteria, G⁺/G^-), enzyme activity (glucosidase, βG; β-N-Acetylglucosaminidase, NAG; acid phosphatase, AP), chemical element content and stoichiometry in root and leaf debris (3 years after decomposition) of Cunninghamia lanceolata to nitrogen and phosphorus additions. Results showed that Cy/pre, F/B, G⁺/G^- were lower and Mono/sat was higher in the leaf debris than those in the root debris. However, nitrogen and phosphorus additions had no significant effect on the microbial community structure of the debris. The leaf debris had higher βG and NAG activity and βG/AP compared with the root debris. Nitrogen and phosphorus additions decreased the AP activity and increased βG/NAG and βG/AP. Moreover, nitrogen and phosphorus additions resulted in a greater decrease in root debris' AP activity but a more significant increase in βG/NAG of leaf debris. Multiple stepwise regression showed that Mono/sat, G⁺/G^- and F/B positively correlated with manganese content, phosphorus/calcium, and nitrogen content, respectively. AP and βG/NAG were positively correlated with nitrogen/phosphorus and phosphorus/iron, respectively; and βG/AP, NAG, and βG were negatively correlated with nitrogen/manganese, phosphorus/magnesium, and nitrogen/calcium, respectively. Our results found that the effects of nitrogen and phosphorus additions on microbial community structure and enzyme activity were generally inconsistent between root and leaf debris, thereby underlining that leaf and root litters need to be considered separately when evaluating the response of decomposers to their substrates in the context of global change to improve the prediction accuracy of ecosystem nutrient cycling processes.