A preparative high-speed counter-current chromatography (HSCCC) method for isolation and purification of silychristin, silydianin and taxifolin in the co-products of the silybin refined process from the silymarin was successfully established by n-hexane–chloroform–methanol–water (0.5:11:10:6 (0.5 acetic acid), v/v/v/v) as the two-phase solvent system. 146mg silydianin, 280mg silychristin and 63mg taxifolin from 1.463g co-products sample in one separation were obtained with the purities of 95.1%, 99.3% and 98.2%, respectively, determined by HPLC. The structures of the compounds were identified by means of ESI-MS-MS, TOF-MS, 1 H NMR, 13 C NMR and 2DNMR-HMBC. Silychristin, silydianin and taxifolin had been separated as standards by HSCCC for the first time. A comparative study between HSCCC and RPLC for separation and isolation of taxifolin, silychristin and silydianin was investigated. The differences between the two preparative chromatographic methods were all discussed. The results demonstrated that HSCCC was a powerful separation tool and could contribute to identifying and quantifying plant ingredients.