As living standards improve, obesity has become an increasingly serious health problem. Natural extracts from a wide range of sources are non-toxic and have significant potential as drugs for the prevention and treatment of obesity. We assessed 243 natural small molecules in a HepG2 fat accumulation model and found that epigoitrin (EP) from Radix isatidis reduced intracellular fat deposition, increased short-chain acyl CoA dehydrogenase (SCAD) activity, promoted glucose uptake and glycogen storage, increased ATP production and reduced glutathione (GSH) content, reduced reactive oxygen species (ROS), and enhanced superoxide dismutase (SOD) activity. In a murine high-fat diet model, the addition of EP to the high-fat diet significantly reduced fat deposition, increased glucose tolerance, improved insulin sensitivity, and increased energy expenditure. In conclusion, EP alleviated obesity caused by a high-fat diet and improved disorders of lipid and glucose metabolism.