Climate change and anthropogenic changes in net plant primary production affect above- and belowgroundcarbon inputs to forest soils, in which microbial communities play a key role. Picea schrenkiana forests are important ecological barriers and valuable biological resources in the Tianshan Mountains. Investigating the response of microbial-mediated soil nutrient cycling to exogenous carbon input has great theoretical value. Therefore, in this study, we investigated the changes in soil nitrogen (N) and phosphorus (P) cycling pathways and functional genes in the spruce forest area of Picea schrenkiana via a 6-year field manipulation experiment by using metagenomic sequencing technology. The results revealed that the double litter treatment resulted in a greater abundance of functional genes involved in N and P cycling and significantly increased the relative abundance of assimilation (nasA), ammonification (ureC), and P uptake and translocation processes (plpQ and phnE). The no-root treatment significantly increased the relative abundance of soil nitrification (amoA), denitrification (nirK) and P starvation response regulation (phoR and phoB). In the network, the no-root treatment presented the greatest number of network topology attributes, and key genes were influenced mainly by the soil total nitrogen and electrical conductivity. Pathway analysis revealed that microbial diversity had a significant direct effect on the abundance of N and P cycling genes. These insights deepened our understanding of the N and P cycle in arid zone montane forest ecosystems and provided a biological perspective on the microbial genetic potential of soil N and P cycle under different long-term carbon inputs.