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Aims Degradation of alpine meadows on the Qinghai-Tibet Plateau is a major issue affecting both ecology and economy. Microorganisms play an important role in soil nutrient cycling and regulation of ecosystem function. This study aimed to investigate the species composition and diversity of microbial communities, and understand the response of microbial communities to changes in physicochemical properties resulting from meadow degradation. Methods In this study, the soil bacterial and fungal communities and diversity of alpine meadows of degradation gradient were sequenced by high-throughput sequencing. The function of microbial communities was predicted with Picrust2 and FUNGuild. Results As meadow degradation increased, there were 36 bacterial taxa and 28 fungal taxa showing significant differences. The relative abundance of meadow pathogenic fungi increased significantly (P < 0.05). Bacterial and fungal α- diversity mostly tended to decrease. Picrust2 analysis showed a decrease in synthesis-related functional gene abundance and an increase in metabolism-related functional gene abundance. FUNGuild analysis showed that symbiotic and saprophytic symbiotic nutrient fungi decreased significantly (P < 0.05). The pH and available nutrients were identified as the main drivers of changes in the structure, of microbial communities. Conclusion The degradation of meadows directly affects soil nutrient content, which in turn affects the diversity and function of soil microbial composition. The combined effect of soil nutrient reduction and microbial community changes reduces the stability of meadows. This work reveals the response and main environmental drivers of alpine meadow degradation in microbial communities, which provides theoretical support for the conservation and sustainable development of alpine meadows.