Soil microbes play a critical role in maintaining the health and stability of these ecosystems. However, the ecological assembly processes of soil microbial communities remain poorly understood. This study explores the changes in ecological components across original and degraded patches of alpine meadows in Sanjiangyuan National Park and analyzed soil microbial community structure using high-throughput sequencing techniques. Results showed that alpine meadows degradation increased vegetation species diversity, significantly reduced aboveground productivity, and made the soil more barren and alkaline. Although the dominant phyla of soil microorganisms were similar across different degradation states, degradation significantly increased the relative abundance of oligotrophic bacteria and decreased the relative abundance of dominant fungi. Additionally, microbial communities exhibited significant β-diversity. Degradation also led to an increase in microbial α-diversity, heightened microbial taxa competition and a more complex microbial co-occurrence network. However, vegetation-soil variables explained only a small portion of the variation in soil microbes. Through the study of microbial ecological assembly processes, we found that degradation enhanced the stochastic processes of soil microbial communities, and the changes in soil microbial communities were mainly driven by the variations inherent in the microbes themselves. These findings highlight the complex ecological interactions between above- and belowground components and emphasize the critical role of microbial community dynamics in mediating ecosystem functions.