Room-temperature ionic liquids (ILs) are liquids that are constituted entirely of ions and can provide a solvent environment quite unlike any other available at room temperature. They continue to attract considerable interest in the chemistry research community as they are good solvents for a wide range of both inorganic and organic materials. In this study, a CZE method has been established for resolving natural flavonoids, quercetin, kaempferol and isorhamnetin in the Chinese herbal extract from Hippophae rhamnoides and its medicinal preparation (Sindacon Tablet). In this method, 1-alkyl-3-methyl-imidazolium-based ILs are used as the additive, and the effects of the alkyl group, imidazolium counterion (anionic part), along with the concentration of IL are investigated and discussed. Baseline separation, high efficiencies and symmetrical peaks of the three flavonoids were obtained. The separation mechanism seems to be the hydrogen-bonding interaction between the imidazolium cations of IL and the flavonoids.