Abstract: To investigate the effect of plant diversity on soil fungal communities, we conducted a three-year experiment in an alpine meadows on the Qinghai-Tibet Plateau. The experiment included five treatments: no removal, legume and forb removal, graminoid and forb removal, graminoid and legume removal, and all removal. We analyzed soil fungal abundance and diversity using high-throughput sequencing, and measured root and soil properties. Results showed that Ascomycota, Mortierellomycota, and Basidiomycota were the dominant fungal phyla in the different treatments, accounting for more than 90%. There were no significant differences in composition and alpha diversity indices of the fungal communities under different treatments. The relative abundance of Glomeromycota was increased under graminoid and forb removal and graminoid and legume removal. Compared to the other treatments, the removal of graminoids and forbs increased the relative abundance of Zoopagomycota. The dominant fungal functional group was soil saprotroph fungi in all treatments. The relative abundance of arbuscular mycorrhizal fungi was increased under legume and forb removal and graminoid and forb removal. Compared with the removal of all, the removal of graminoids and legumes increased the relative abundance of lichen parasites/saprotroph fungi. The Mantel test showed no clear correlation between soil fungal community composition and function and environmental factors. Soil fungal richness indices were negatively affected by the increase in root biomass, root carbon:nitrogen (C:N), and dissolved organic carbon. Overall, our results indicate that the removal of plant functional groups in alpine meadows on the Qinghai-Tibet Plateau has a significant effect on soil fungal community structure but not on fungal community diversity.