Soil microbes provide important ecosystem services. Zoige Plateau wetland, the largest alpine peat wetland in the world, has suffered from serious degradation in the past 30 years. We studied the composition of the Zoige Plateau alpine wetland soil microbiota and relations among specific taxa using 16S rRNA amplicon sequencing combined with association network analysis. Compared to the pristine swamp soil, taxons DA101, Aeromicrobium, Bradyrhizobium, and Candidatus Nitrososphaera were enriched and several methanogenic Euryarchaeota were depleted in the moderately degraded meadow soil and highly degraded sandy soil. Soil total potassium contents in soils with different degradation levels were significantly different, being the highest in meadow soil and lowest in swamp soil. The association network analysis showed that total potassium positively correlated with specific bacterial and archaeal taxa. Jiangella, Anaerolinea, Desulfobulbus, Geobacter, Flavobacterium, Methanobacterium and Methanosaeta were identified as the keystone genera in the networks. Soil degradation affected soil properties, and caused changes in the bacterial and archaeal community composition and the association patterns of community members. The changes could serve as early warning signals of soil degradation in alpine wetlands.