Rodent disturbances are considered as the key factors that affect grassland ecological restoration worldwide. Although the impact of rodent disturbances on plant diversity and ecosystem functions has been extensively studied, our understanding of how such activities shape soil bacterial community networks and their functional roles remains limited. In this study, we employed 16S rRNA sequencing to investigate soil bacterial communities between undisturbed alpine meadow and zokor mounds at different successional stages. Additionally, we analyzed the co-occurrence networks and potential functions within the alpine meadow ecosystem. The results revealed that (1) the disturbance by plateau zokors altered the soil bacterial community structure, increased bacterial diversity and reduced network complexity. Also, there were synergistic interactions among key species in the soil bacterial co-occurrence network; (2) soil organic carbon (SOC) and total nitrogen (TN) were identified as the key environmental variables that shape soil bacterial communities; (3) functional predictions based on FAPROTAX indicated that the disturbance by plateau zokors significantly affected the functional groups involved in carbon (C) and nitrogen (N) cycling. Overall, these findings significantly enhance our understanding of how small mammal activities influence the soil nutrient cycling and bacterial community in the Qinghai-Tibet Plateau (QTP) alpine meadow.