In this study, a valid method was established for the isolation and purification of flavone glycosides from Hippophae rhamnoides L. seed residues using high-speed counter-current chromatography in one step, with a solvent system of ethyl acetate-methanol-n-butyl alcohol-water (9:1:0.5:9, v/v/v/v). A total of 28.8 mg compound I and 57.3 mg compound II were obtained from 200 mg of flavone H-glycosides rich extract, with purities of 98.3 and 96.4%, respectively. The structures of two compounds were identified by MS and NMR. 3-O-β-D-Sophorosylkaempferol-7-O-{3-O-[2(E)-2,6-dimethyl-6-hydroxyocta-2,7-dienoyl]}-α-L-rhamnoside is compound I and compound II named hippophanone is a new compound were identified by MS and NMR. The method was efficient and convenient, which could be used for the preparative separation of flavone glycosides from H. rhamnoides L. seed residues.