Natural products are normally obtained by organic solvent extraction and many subsequent chromatographic separations. Compounds of interest are often isolated with very low yield and limited purity. An aqueous two-phase extraction process combined with a simple ethanol treatment, for removing excess inorganic salt, has been developed for preparation of geniposide from gardenia. The system was comprised of PE62, a random copolymer composed of 20% ethylene oxide and 80% propylene oxide, KH2PO4 and ethanol. To find optimal conditions, the partition behavior of geniposide under an aqueous two-phase system was investigated. Various factors were considered, including the concentration of salt, the concentration of polymer, the sample loading, and the addition of ethanol. The experimental results demonstrated that increasing salt concentration or decreasing PE62 concentration results in enhancement of the geniposide partition in the salt-rich phase. The addition of ethanol and higher sample loading also promoted the partition efficiency of geniposide. Based on this study, an optimized system containing 5% PE62, 7.5% KH2PO4, and 10% ethanol was tested on a large-scale extraction. A 39.0-g aliquot of final product (in powder form) with 77% purity of geniposide can be effectively extracted from 500 g of gardenia fruit. This process is proved to be useful for industrial application of geniposide preparation.