With the interaction between global climate change and unreasonable human utilization, the alpine meadows on the Qinghai-Tibet Plateau have suffered various weathering degrees. Uncovering the degradation mechanism and restoration strategies can be facilitated by gaining insights into the diversity of soil microflora during meadow degradation. Therefore, we used Illumina sequencing technology to investigate the patterns of soil microbial diversity, microbial community composition, and the driving factors of microbial change in all non-degraded (ND), lightly degraded (LD), moderately degraded (MD), and severely degraded (SD) alpine meadows in the southeastern Qinghai-Tibet Plateau. Our results pointed out that with the intensification of degradation, vegetation characteristics were significantly reduced, and soil parameters significantly varied among all degraded meadows. The contents of soil organic carbon (SOC), total nitrogen (TN), available phosphorus (AN), and total phosphorous (AK) in soils decreased with the increase of degradation. The dominant bacterial phyla were the same regardless of the meadow degradation level with Actinobacteria (37.67%) and Proteobacteria (20.62%) having the highest relative abundance. Meanwhile, the dominant fungi were Ascomycota (49.9%). Based on the linear discriminant analysis (LDA) and effect size (LEfSe) method, 38 bacterial and 49 fungal species were found to be affected in the degraded alpine meadow, most of which belonged to Actinobacteria and Ascomycota, respectively. Mantel test analysis illustrated that the bacterial community was mainly significantly dependent on below-ground biomass, pH, soil organic carbon, and total nitrogen, while the fungal community was significantly dependent on soil organic carbon, total nitrogen, available nitrogen, and available potassium. These results suggest that the degeneration of alpine meadows contributes to the variability of the diversity and composition of microflora on the Tibetan plateau. Yet this effect is mainly dependent on soil factors.