A preparative high-speed countercurrent chromatography method was successfully used for the isolation of five minor flavones from Polygonum cuspidatum flowers. Among them, three compounds were obtained from P. cuspidatum for the first time. A twin two-phase solvent system composed of n-hexane/ethyl acetate/ethanol/water (1: 6: 3: 6, v/v/v/v) and petroleum ether/ethyl acetate/methanol/water (2: 4: 3: 3, v/v/v/v) was developed. Compounds were obtained from the fraction B and fraction C prepurified by silica gel column chromatography. Five minor compositions, 6.8 mg of hesperidin, 11.2 mg of phloridzin, 4.9 mg of luteolin, 5.3 mg of hyperin, and 3.7 mg of luteoloside were obtained from 140 mg of the fraction B and 110 mg of fraction C with a purity of 95.3, 96.4, 98.0, 96.8, and 95.3%, respectively, as determined by high-performance liquid chromatography. The structures of these compounds were identified by H-1 and C-13 NMR spectroscopy.