The unique flavor and health-care function of koumiss are closely related to its complex microbial structure. In this study， metagenomic technology was used to analyze the microbial diversity and functional genes of koumiss. The results showed that 30 phyla， 331 families， 913 genera and 2 692 species were identified. The dominant strains were Lactobacillus kefiranofaciens， Lactobacillus helveticus， Citrobacter freundii， Raoultella ornithinolytica， Citrobacter werkmanii and Lactococcus lactis. 10 849 and 214 338 genes were respectively annotated by COG and KEGG databases， the prominent pathways were carbohydrate metabolism and amino acid metabolism， followed by metabolic activities such as co-enzyme factor and vitamin metabolism and nucleotide metabolism. After CAZy database annotation， the number of glycolytransferases (1 238) and glycolytic hydrolases (1 430) was the highest， accounting for 76% of the active carbohydrate enzymes of koumiss. At the same time， three RRT12 proteases， two serralysin metalloproteinases， type 6 protein secretion system (T6SS) genes， 232 peptide transport systems and 231 peptidase control genes were found in koumiss， which showed strong protein decomposition and transport potential. Further， there were 26 ArAT genes， 40 ketoacid invertase genes， 51 AlcDH genes， 68 AldDH genes and 34 aes genes encoded in koumiss， which have the basis of forming strong flavor substances from amino acids.