Lake Caohai is a complete and typical plateau lake wetland ecosystem formed by the accumulation of water in the karst basin. It is also the largest karst structural lake in China. Methanotrophs is a kind of unique microorganisms that can oxidize methane to CO₂ and water. Their activities are inseparable from the key steps of energy flow and element cycle in the ecosystem. In order to understand the community structure and function of methanotrophs in the wetland of karst Lake Caohai, Guizhou Plateau, we used metagenomics technology to study shallow-water marshes, sedge wetlands, and deep-water sediments. The results showed that the main aerobic methanotrophs in the Lake Caohai wetland were Methylobacter and Methylomonas, and the main anaerobic methanotrophs were Candidatus_Methylomirabilis_oxyfera, which belonged to the NC10 denitrifying anaerobic methanotrophs. The diversity of the four metabolic function genes studied is carbon metabolism>nitrogen metabolism>sulfur metabolism>methane metabolism; based on the KEGG database, a total of 6 categories of functions and 18 complete metabolisms related to carbon, methane, nitrogen, and sulfur are annotated path. PCoA analysis showed that the types and functions of methanotrophs in shallow-water marshes and sedge wetlands are similar and different from those in deep-water sediments. Species and function correlation network analysis results show that Methylacidiphilum_fumariolicum and Methylacidiphilum_kamchatkense have strong correlations with the various metabolic functions in the Lake Caohai wetland. The environmental factors that significantly affect the community structure of methanotrophs in Lake Caohai wetland are nitrate, electrical conductivity, total phosphorous and soil organic matter.