Livestock grazing can alter biodiversity and ecosystem functions. However, how long-term and continuous grazing intensity affect belowground biodiversity remains unclear, especially for soil microbial diversity. Here, through a well-controlled 5-year field experiment in a Tibetan alpine meadow, the responses of soil bacterial and fungal communities to yak grazing intensity were examined. Our results showed that grazing intensity significantly changed soil bacterial and fungal community compositions, rather than microbial α-diversity. The co-occurrence network analysis indicated that both soil bacterial and fungal network complexity gradually decreased with increasing grazing intensities. Meanwhile, soil C/N ratio, soil moisture, dissolved organic nitrogen (DON), NH₄⁺-N, and aboveground biomass (AGB) were related to soil bacterial community, and AGB, NO₃^--N, NH₄⁺-N, and DON and were associated with soil fungal community. Taken together, our manipulative experiment provides empirical evidence that grazing intensity-induced alterations of aboveground vegetation and nitrogen availability primarily trigger the shift of soil microbial community and structure. These results can support grassland management and ecological restoration in alpine ecosystems.