Taeeumjowuitang (TJ) is an alternative herbal medicine that has been used to treat obesity in Korea. The molecular mechanisms involved in TJ-induced anti-obesity effects have not yet been determined. The aim of the current study was to elucidate the effects of TJ on obesity and metabolic syndrome, by analyzing the transcriptional and metabolic responses to TJ treatment. C57BL/6J mice were fed a high-fat or high-fat + 3% (/) TJ diet for 12 weeks. Their phenotypic characteristics were measured and the anti-obesity mechanism was elucidated, based on the RNA sequencing (RNA-seq) transcriptomic profiles in an animal model of obesity. TJ treatment ameliorated insulin resistance, dyslipidemia, and hepatic steatosis in high-fat diet-induced obese mice, with a simultaneous reduction in body weight gain by enhancing energy expenditure and suppressing adiposity. An analysis of the global transcriptional changes by RNA-seq revealed that TJ upregulated mitochondrial oxidative phosphorylation-associated genes in epididymal white adipose tissue (eWAT), suggesting an enhanced mitochondrial function after TJ treatment. Moreover, TJ effectively attenuated the high-fat diet-induced inflammatory response through transcriptional changes in eWAT. Our findings provide some mechanistic insights into the effects of TJ, an alternative oriental medicine, in the treatment of obesity and its comorbidities. They demonstrate that metabolic and transcriptional responses to diet-induced obesity with TJ treatment were desirable in adipose tissue metabolism.