Kombucha is a traditional beverage obtained from fermented sugar-tea by a community of bacteria and yeasts. Understanding the microbial composition and their functions in Kombucha fermentation is of significance, but most of the studies have relied on the culture-dependent method. In this study, a metagenomic analysis was conducted to obtain a more comprehensive insight into Kombucha fermentation. Results showed that the bacteria of Kombucha were dominated by Komagataeibacter (36.24 to 63.35%), Gluconacetobacter (10.39 to 26.21%), Gluconobacter (6.62 to 27.10%), Acetobacter (0.3 to 6.64%), and the fungus Kluyveromyces (0.63 to 36.98%) was also identified. Taxonomic composition and abundance of the microbial community were distinct with each Kombucha sample. The carbohydrate active enzyme functions of the communities primarily comprised glycosyltransferase (GT) families (40.6%), glycoside hydrolase (GH) families (32.0%), and carbohydrate-binding module (CBM) fam-ilies (12.9%). Moreover, functional genes and their KEGG pathways were predicted, which demonstrated that the functional genes present in the bacterial community were enriched in pathways for neurodegenerative disease, amino acid metabolism, metabolism of cofactors and vitamins, carbohydrate metabolism, folding, sorting and degradation, and translation. The results of this study would provide a better understanding of the microbiota and metabolites as well as health-promoting potential of Kombucha, and may facilitate the optimization of the process to produce Kombucha products with desirable qualities.