An alcohol/salt aqueous two-phase system (ATPS) composed of 1-propanol and (NH4)2SO4 was employed to purify anthraquinones (AQs) extracted from Aloe vera L. The main influencing system parameters such as type of alcohol, type and concentration of salt, temperature and pH were investigated in detail. Under the optimal extraction conditions, AQs can be extracted into alcohol-rich phase with high extraction efficiency, meanwhile majority polysaccharides, proteins, mineral substances and other impurities were extracted into salt-rich phase. Partitioning of AQs is dependent on hydrophobic interaction, hydrogen bond interaction, and salting-out effect in ATPS. Temperature also played a great role in the partitioning. After ATPS extraction, alcohol can be recycled by evaporation; moreover, salt can be recycled by dilution crystallization method. Compared with other liquid-liquid extractions, this alcohol/salt system is much simpler, lower in cost with easier recovery of phase-forming components, which has the potential scale-up in down-processing of active ingredients in plant.