To explore mild and efficient techniques for separation and purification of the active ingredients in natural plants is still ongoing. Ionic liquid (IL) is a new class of molten salts that are liquid at ambient temperature, which has many unique properties is safe and environmentally friendly chemical. Aqueous two-phase systems (ATPSs) based on ILs and salts were applied to isolate and purify anthraquinones (AQs) from aloe leaves. The main affecting parameters on the partitioning behavior and extraction efficiency were investigated through the partitioning process: type and mass of salt, pH, extraction temperature, and equilibrium time of the systems. Aloe AQs preferentially migrated into the IL-rich phase. Under the optimal conditions, the maximal extraction efficiency 92.1% of total AQs was obtained with the [C4mim]BF4/Na2SO4 system at 25 °C and pH 4.0. The reverse extraction experiments were done by adjusting pH with IL being recycled. Furthermore, the major constituents of aloe-emodin and chrysophanol were analyzed by a HPLC method. Ionic liquid-based ATPSs (ILATPSs) are great candidates for the replacement of volatile organic compounds in typical liquid–liquid extraction. This proposed extraction technique opens up new possibilities in purification of other active ingredients in natural plants or biologic samples.