The soil microbial functional community is a better predictor of ecosystem processes under global change. However, the responses of the soil microbial functional community structure to short-term nitrogen (N) and phosphorus (P) additions remain unclear. Here, we carried out an experiment exploring the effects of N and P additions on soil fungal and bacterial functional diversity and community composition in an alpine steppe on the Tibetan Plateau. The results showed that soil fungal functional α-diversity significantly decreased under N or P addition, whereas soil bacterial functional α-diversity did not change. Furthermore, soil bacterial functional group aerobic nitrite oxidation increased significantly under combined N and P additions, but soil bacterial and fungal community composition and β-diversity did not change. Further analysis illustrated that soil available nitrogen was the main factor leading to the changes in soil fungal functional α-diversity and soil bacterial functional groups under N and P additions. Therefore, we should give importance to the potential influence in view of future increasing N and P deposition on the soil microbial functional community in the alpine grassland on the Tibetan Plateau, which will be beneficial for the prediction of soil biogeochemical cycles and guiding ecosystem management.