This study employs the synchronized multi-point field sampling to investigate the influence of plateau pika disturbance on the beta diversity of plant species and functional traits in alpine meadows. We identify the pathways of change in the beta diversity of both species and functional traits under plateau pika disturbance, and outline strategies for maintaining plant diversity in alpine meadows, within regions disturbed by plateau pikas based on plant species diversity and functional trait diversity. The results demonstrate that the plateau pika disturbance significantly decreases the similarity of plant species by 28.1% and functional trait similarity by 28.7%. Although plateau pika disturbance does not alter the pathways of change in species and functional trait beta diversity and does not have a significant impact on the nestedness component of species and functional traits, the disturbance significantly reduces the proportion of turnover components in both plant species and functional traits by 36.6% and 34.3%, respectively. Within regions disturbed by plateau pikas, the variation in species beta diversity in alpine meadow plants is largely attributed to turnover (turnover accounts for 81.4%; nestedness accounts for 18.6%). In contrast, the change in functional trait beta diversity is predominantly driven by nestedness (nestedness accounts for 64.9%; turnover accounts for 35.1%). Consequently, for the designated plateau pika disturbance zones, it is necessary to protect all plateau pika habitats within these regions (multi-site protection) to achieve the goal of maintaining plant species diversity. Meanwhile, maintaining a high level of plant functional diversity can be achieved by emphasizing on protecting sites within the region that are rich in plant functional traits.