The selective feeding of plants and excavation of soil by small mammals, especially rodents, have important effects on plant-animal interactions, but few studies have explored these effects and their potential mechanisms. In the present study, large-scale enclosure manipulative experiments were performed to explore the effects of Brandt’s vole (Lasiopodomys brandtii) on plant community composition and soil nutrients in Inner Mongolia, China. The results suggested that Brandt’s vole significantly decreased community biomass compared to the control enclosure, reducing it by 21.42% at the end of the experiments. Further analysis showed that the rhizome grass biomass was significantly reduced by 86.82%, while the biomass of bunch grasses and forbs was higher in the vole enclosure by 18.35% and 49.64%, respectively. Furthermore, Brandt’s vole significantly decreased species richness and the density, coverage, and importance value of the main forage species available. However, the soil main nutrient content and ammonium nitrogen mineralization rate were not significantly affected by the presence of Brandt’s vole, whereas nitrification rate significantly increased in the vole enclosure. Finally, we conclude that Brandt’s vole activity may affect the species’ habitat quality by creating plant communities dominated by less preferred forage species.