To investigate the effect of ionic liquids (ILs) as additives to a two-phase solvent system using high-performance counter-current chromatography, the two structurally similar flavonoids, Kaempferol-3, 4-di-O--D-glucoside and Kaempferol 3-O--D-(2-O--D-glucosyl)-glucopyranoside, were chosen as models. The effects of the length of the alkyl groups on the imidazolium ring and its counterion, and the concentrations of ILs on the K values were investigated. The results showed that the K values of the target compounds could be improved when ILs were used as additives in the two-phase solvent system. The mechanism of ILs as additives to the solvent system was discussed for the first time.