The present invention relates to a novel use of a panduratin derivative or a Boesenbergia pandurata extract. More specifically, the invention relates to a composition for preventing and treating/relieving a metabolic disease selected from a group consisting of obesity, hyperlipidemia, hypercholesterolemia and diabetes, containing a panduratin derivative represented by Chemical Formula 1, 2 or 3 or a Boesenbergia pandurata extract as an active ingredient, a method for treating a metabolic disease selected from a group consisting of obesity, hyperlipidemia, hypercholesterolemia and diabetes, by administering an effective amount of the panduratin derivative or the Boesenbergia pandurata extract to a subject in need thereof, and a use of the panduratin derivative or the Boesenbergia pandurata extract to prepare a reagent for preventing and treating/relieving a metabolic disease selected from a group consisting of obesity, hyperlipidemia, hypercholesterolemia and diabetes. As can be seen foregoing, the present invention provides a novel use of a panduratin derivative or a Boesenbergia pandurata extract. A panduratin derivative or a Boesenbergia pandurata extract of the present invention shows excellent effects on a metabolic disease such as obesity, hyperlipidemia, hypercholesterolemia and diabetes by decreasing highly related causes of metabolic diseases such as on weight, body fat and lipid-content. Since a composition of the present invention is originated from natural materials, it can be used without side effect and provides novel method for preventing and treating/relieving a metabolic disease through body weight loss and body fat loss and the like.