The invention discloses a method for preparing a flavonoid glycoside and stibene glucoside type compound by separating from fenugreek. By virtue of a high-speed countercurrent chromatography (HSCCC) separation technology, isomerides such as vitexin and isovitexin and stibene glucoside type compounds such as rhaponticin, deoxyrhapontin and rhapontigenin which have the similar polarity to that of the isomerides in the fenugreek are subjected to separation preparation, so that the separation time is effectively shortened, and the shortcomings of complicated operation, sample die-adsorption loss, low yield and the like of the conventional preparation method are overcome. According to the method, the technology is simple, the reproducibility is high, and the separation efficiency is high; the obtained monomer content is higher than 96.0 percent and can meet the requirements of a type of botanical drugs and standard contrasts; and the method is suitable for industrial production of medical medicines, standard substances, health protection food, health protection medicines and the like.