Due to the low viscosity of the carbon dioxide, supercritical-fluid chromatography (SFC) allows higher flow rates with lower back pressure, usually analytical SFC can provide much faster and more efficient separation compared to conventional chromatographic methods. The non-polar character of supercritical carbon dioxide (scCO2) limited SFC in separate hydrophobic compounds, but various modifiers can be used to improve the selectivity of SFC. Ionic liquids (ILs) exhibits various features including wide range of solubility, miscibility, high thermal stability, and low vapor pressure, were widely used as additive to modify the character of mobile phase, but the performance of ILs in improving SFC separation has not been evaluated. In this work, analytical SFC was applied for the separation of six flavonoid aglycones, 1-butyl-3-methyl imidazolium-based ILs were tested and compared as the mobile phase additives. ILs could significantly improve the resolution of flavonoid aglycones and the selectivity changed probably based on the hydrogen-bonding interaction.