Pu-erh tea, a traditional Chinese beverage, performs an anti-obesity function, but the correlation between its components and efficacy remains unknown. Here, we screened two Pu-erh teas with significant anti-obesity efficacies from 11 teas. In vitro experiments revealed that lipid accumulation in L02 cells and lipid synthesis in 3T3-L1 cells were significantly better inhibited by Tea-B than Tea-A. Further in vivo experiments using model mice revealed that the differences in chemical components generated two pathways in the anti-obesity efficacy and mechanism of Pu-erh teas. Tea-A changes the histomorphology of brown adipose tissue (BAT) and increases the abundance of Coriobacteriaceae_UCG_002 and cyclic AMP in guts through high chemical contents of cyclopentasiloxane, decamethyl, tridecane and 1,2,3-trimethoxybenzene, eventually increasing BAT activation and fat browning gene expression; the high content of hexadecane and 1,2-dimethoxy-benzene in Tea-B reduces white adipose tissue (WAT) accumulation and the process of fatty liver, increases the abundance of Odoribacter and sphinganine 1-phosphate, inhibits the expression of lipid synthesis and transport genes. These mechanistic findings on the association of the representative bioactive components in Pu-erh teas with the anti-obesity phenotypes, gut microbes, gut metabolite structure and anti-obesity pathways, which were obtained for the first time, provide foundations for developing functional Pu-erh tea.