To explore convenient and efficient techniques for the extraction and separation of the active ingredients in medicinal plants is still ongoing. As a new class of molten salt, ionic liquids (ILs) are widely used in the extraction of bioactive compounds from plant resources. In this work, the IL-based biphasic system was developed for the extraction and separation of the homologues of baicalin and baicalein from Scutellaria baicalensis Georgi. The IL-water biphasic system is superior to the other organic solvents-water systems for the extraction and separation of baicalin and baicalein. The phase volume ratio of the IL-water biphasic system was studied, and the other influencing parameters of solid-liquid ratio, extraction temperature, extraction time, and ultrasonic time were optimized through the single factor experiments. The results revealed that the extraction yields were 43.3 mg/g and 14.3 mg/g for baicalin (aqueous phase) and baicalein (IL phase), respectively; and the distribution co-efficients were 23.8 and 13.7 for baicalin and baicalein, respectively under the optimized conditions. Finally, the IL can be easily recycled and reused by means of its temperature-responsive characteristic. This study provides a green and efficient method for the selective separation of the homologues in natural plant resources.