As the hot spot of nitrogen (N) and phosphorus (P) deposition in the subtropical of China, the response of forest ecosystem carbon (C), N and P cycle to N and P deposition has got more and more concerns. As an important source of supplying of soil C and nutrients in forests, root input variations regulated the process of soil C and nutrient cycle by affecting soil enzyme activity under N and P deposition. Ammonium nitrate and sodium dihydrogen phosphate were added in moso bamboo forest as N and P addition to simulate N and P deposition in our study, respectively, and a total of four treatments were set up:control, N addition, P addition, and N+P co-addition. Combined with root exclusion treatment, the effects of root exclusion and N and P addition on soil C, N and P related enzyme activities were explored, and their relationships between soil C, N and P related enzyme activities and soil and fine root chemical properties were analyzed for further. The results showed that the response of soil C and N related enzyme activities to root exclusion was more sensitive than those to N and P addition in general, which caused from the negative response of soil total nitrogen and ammonium nitrogen to root exclusion, but the neutral response of soil organic carbon, total nitrogen and ammonium nitrogen to short-term N and P addition. Different from the activities of C and N related soil enzyme to root exclusion and N and P addition, soil P related enzyme activities showed a negative response to root exclusion and phosphorus addition, respectively, which may be attributed to decline in microbial P mining effect. Because preventing of root P absorption caused from root input variations in trench plots and supplementing of soil P under P addition and N+P co-addition treatments may reduce the utilization of soil P by microorganisms in our study site. Despite all this, soil microorganisms are still suffering from P limitation under P addition treatment in our study area, and the main reason is that the underground root system has stronger P absorption and utilization capacity than microorganisms in the P-deficient moso forest ecosystem. Our results highlight the discrepancy of the responses of multiple functional soil enzyme activities to soil nutrients addition and root input variations, and provide a basis for predicting soil C and nutrient cycling in low-P moso bamboo forest ecosystem.