Soil microbial communities are susceptible to perturbations by small mammalian herbivores, such as Brandt's voles (Lasiopodomys brandtii), through their foraging and burrowing behaviors. The interaction between these activities and climate change factors, particularly increased rainfall, can profoundly affect the structure and functions of soil microbial communities. However, the mechanisms by which soil microbial communities respond to small mammalian herbivores under climate change remain poorly understood. In this study, a 9-year manipulative experiment was conducted within a temperate steppe ecosystem to investigate these interactions under increased rainfall conditions. The results indicated that rainfall intensity modulated the impact of vole activity on soil microbial communities. The bacterial community showed an sensitivity to both vole activity and increased rainfall, whereas the fungal community remained relatively stable in terms of composition, functions and network. Vole activity resulted in a significant reduction in the diversity of the bacterial community, accompanied by alterations in its composition and network complexity. Light rainfall exacerbated the negative effects of voles on soil bacterial diversity, while moderate rainfall partially mitigated these impacts. Furthermore, our study found that the relative abundance of bacterial functional groups responded significantly to both vole activity and rainfall addition (P < 0.05). The changes of bacterial community composition were mainly attributed to shifts in the copiotrophic taxa Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. The direct effects of rainfall and vole activity were the primary pathways of soil bacterial diversity changes. Additionally, increased rainfall may reduce bacterial diversity indirectly by elevating soil pH. Overall, our study provides valuable insights into how burrowing rodents and climate change interact to disrupt grassland soil subsystems, highlighting the potential for climate change to modulate the ecological impacts of small mammalian herbivores.