High-speed counter-current chromatography was used to separate and purify flavonoids from the ethyl acetate extract of Oroxylum indicum. After the optimization of separation conditions on analytical instrument, including the two-phase solvent system, rotation speed, flow rate, sample volume and sample concentration, a linear scale-up procedure was performed at preparative grade. Chrysin (160.9 mg, 97.3% in purity), baicalein (130.4 mg, 97.6% in purity), baicalein-7-O-glucoside (314.0 mg, 98.3% in purity), baicalein-7-O-diglucoside (179.1 mg, 99.2% in purity), and a new chrysin-diglucoside (21.7 mg, 98.8% in purity) were obtained from 911.6 mg ethyl acetate extract of Oroxylum indicum by only one step. These five compounds were identified using high performance liquid chromatography, mass spectrometry and nuclear magnetic resonance. With the improvement of the throughput for 53 times after such a scale-up, the resolution and the separation time were kept as the same as those of the analytical grade separation. Therefore, the linear scale-up provided an efficient method for the separation of natural products.