Abstract:[Objective] As an important part of lake ecosystem, microorganisms play an essential role in the biogeochemical cycle of carbon, nitrogen, sulfur, and other elements, and the community structure and functions of them are crucial to environmental stability and sustainability. However, the lakes in Xinjiang are degraded and salinized, and how microorganisms respond to the degradation is unclear. [Methods] The 16S rRNA gene amplicon sequencing was performed to analyze the soil microbial community structure of the degraded area of Barkol Lake and the potential ecological functions of the microorganisms were predicted. [Results] Pseudomonadota, Chloroflexota, and Bacteroidota dominated different parts in the degraded area. In addition, the abundance of Desulfobacterota and Campylobacterota was the highest in the mildly degraded part of the lake, but the two drastically decreased and even disappeared as the degradation aggravated. The extremely degraded part was dominated by Acidobacteriota, Planctomycetota,etc. According to the oxygen utilization predicted by BugBase, the aerobic groups were mainly Actinomycetota, Pseudomonadota, and Chloroflexota, and the majority of them were in the severely degraded part. Moreover, the anaerobic groups were Pseudomonadota, Bacteroidota, and Acidobacteriota, which were mainly in the mildly degraded part. FAPROTAX was employed for predicting the ecological relevant functions of microorganisms in different parts of the degraded area and the result suggested the weakened sulfate respiration, fermentation, and hydrocarbon degradation, and the enhanced nitrification of microorganisms with the aggravation of degradation. [Conclusion] Microorganisms show high diversity in the degraded area of Barkol Lake, which dominate multiple biogeochemical cycles. As the degradation becomes serious, the microbial niche changes. This study lays a theoretical basis for the rational development and utilization of microbial resources in Barkol Lake.