Abstract: Soil microorganisms in Qinghai-Tibet Plateau are highly sensitive to climate change, and freeze-thaw depressions significantly affect soil microbial diversity and carbon and nitrogen metabolism. The surface soil of Wayanshan Heyuan wetland in Qinghai-Tibet Plateau was taken as the research object. The method of macro-genome sequencing was used to explore the effects of freeze-thaw on the composition, diversity and metabolic pathway of soil microorganisms. The results showed that the freeze-thaw depression had no significant effect on the dominant bacteria in soil, but the dominant bacteria were Proteobacteria, Actinobacteria, Planctomycetes and Bacteroidetes, and the fungi were Ascomycota. The freeze-thaw depression significantly reduced the relative abundance of Proteobacteria, increased the relative abundance of Actinobacteria and Ascomycota. Freeze-thaw depression significantly affected soil microbial α diversity, Chao1 index and Richness index were significantly higher than those of natural control, indicating freeze-thaw depression significantly increased the richness of soil microorganisms. The Shannon index was significantly elevated and the Simpson index decreased, indicating freeze-thaw depression improved soil microbial diversity. Freeze-thaw depression significantly increased the gene numbers of amino acid metabolism, carbon metabolism and other metabolic pathways, while decreased those of the two-component system and quorum sensing pathways.