Objective: Bangpungtongseong-san (BT), an oriental herbal medicine, has been used to treat obesity in Korea and East Asian region. The anti-obesity effects of BT have already been studied by several researchers. However, the molecular mechanisms involved in BT-induced anti-obesity effects have not yet been done sufficiently. The aim of this study was to demonstrate the anti-metabolic syndrome effects of BT extract via the analysis or its global transcriptional responses based on mRNA-sequencing. Methods: C57BL/6J mice were fed a high-fat (60% energy as fat), or high-fat + 1.5% (w/w) BT diet for 12 weeks. Results: BT treatment ameliorated insulin resistance, dyslipidemia, and hepatic steatosis in DIO mice, with a simultaneous reduction in body weight gain. And the level of plasma leptin, resistin and pro-inflammatory cytokines was decreased in BT group compared to HFD group. Overall glucose metabolism was enhanced in BT mice compared to HFD mice, including homeostasis model assessment for insulin resistance (HOMA-IR), plasma glucose and insulin concentrations, and hepatic glycogen. Analysis of the global transcriptional changes by mRNA-sequencing revealed that BT supplement resulted in alteration of transcriptional responses associated with lipid metabolism, and carbohydrate metabolism in liver and epididymal white adipose tissue (eWAT). Moreover, BT effectively attenuated the high-fat diet-induced inflammatory response through transcriptional changes in eWAT. Conclusion: Our findings provide some significant insights into the effects of BT for the prevention of metabolic syndrome. We demonstrated that the BT contributed to the regulation of systemic metabolic homeostasis via transcriptional responses in liver and adipose tissue or DIO mice.