Excessive energy intake leads to dysbiosis of intestinal microbiota and puts surrounding tissues under oxidative stress and inflammation, contributing to the development of metabolic syndrome. Taiwanese green propolis (TGP) exhibits a broad spectrum of biological activities, including anti-bacterial, anti-inflammatory, and antioxidant properties. However, the benefits of TGP on metabolic syndrome have not been explained in detail. In this study, we examined the preventive effects of TGP on high-fat diet (HFD)-induced obesity. The results showed that TGP supplementation at 1000 ppm improved condition such as hyperlipidemia, fat accumulation, liver steatosis, and whitening of brown adipose tissue (BAT) in mice. In addition, we observed more cold-induced non-shivering thermogenesis by BAT in TGP treatment with 1000 ppm group. At lower dose of 500 ppm, TGP improved glucose intolerance and insulin insensitivity in HFD mice and restructured the composition of gut microbiota to reduce dysbiosis, which involved an increase in the abundance of metabolism-related bacteria such as Lachnospiraceae NK4A136 group and the decrease in Desulfovibrio. The change of dominant microbiota was associated with the homeostasis of blood glucose and lipid. Transcriptome and micro-western array analysis revealed that TGP supplementation at 500 ppm promoted the browning and adipogenesis in white adipose tissue (WAT), blocked inflammation signaling and attenuated reactive oxygen species, contributing to healthy WAT remodeling and offsetting negative metabolic effects of obesity. We concluded that TGP modulated the function of BAT, WAT, and gut microbiota, bringing a balance to the glucose and lipid homeostasis in the body.