A new process was developed to obtain daidzein, including extraction of isoflavones from the stem of Pueraria lobata (Willd.) Ohwi using n-butanol/water two-phase solvent system, alumina column purification and recrystallization. The effects of solvent type on the extraction yield were investigated. It has been found that 1:1 (v/v) n-butanol/water two-phase solvent system cannot only realize the combination of solid–liquid extraction and liquid–liquid purification, but also result in the maximum yields of daidzein as well as total-isoflavones, compared to the common single-phase extracting solvents.