Preparative high-speed counter-current chromatography (HSCCC) was successfully used for isolation and separation three flavonoids including bolusanthol B, a novel compound named 5,7,2',6'-tetrahydroxy-6,8-di(gamma,gamma-dimethylallyl) flavanone and tetrapterol I from Patrinia villosa Juss using two-phase solvent system composed of n-hexane-ethyl acetate-methanol-water at the volume ratio of 10:11:11:8 (v/v). A total of 25.4 mg bolusanthol B, 52.5 mg 5,7,2',6'-tetrahydroxy-6,8-di(gamma,gamma-dimethylallyl) flavanone and 50.2 mg tetrapterol I were obtained from 250 mg crude extract with purities of 96.8%, 99.2% and 99.3%, respectively determined by HPLC in one single operation and less than 5 h. The structure identification was performed by UV, IR, MS, 1H NMR, 13C NMR and 2D NMR. Among then, bolusanthol B and tetrapterol I were obtained from the plant of Patrinia genius for the first time, and 5,7,2',6'-tetrahydroxy-6,8-di(gamma,gamma-dimethylallyl) flavanone was a novel prenylated flavonoid and discovered from nature for the first time.