A method for preparing flavonoids compounds in camellia seed shells by high-speed counter-current chromatography comprises the following steps: camellia seed shells are taken as raw materials which are crushed and then extracted with ethanol, the extracting solution is collected and purified by D-101 macroporous resin, and after that, the materials of water, n-butyl alcohol, methyl tert-butyl ether, acetonitrile and glacial acetic acid at the volume ratio of 6: 3: 1:1: 0.001 serve as a high-speed counter-current solvent system to conduct high-speed counter-current chromatography on the camellia seed shell extract to prepare two flavonoids compounds. The method is simple and convenient, and excellent in reproducibility, can be used for large-scale preparation of compounds and lays a material basis for further study on activity.