The invention provides a method for conducting double aqueous phase extraction, separation and purification on papain through modified polyethylene glycol-sodium tartrate. The method comprises the steps that papaya juice is subjected to wall breaking through a repetitive freeze-thawing method; supernatant liquor is collected, and a papain crude extract is obtained; modified polyethylene glycol and sodium tartrate are added into the crude extract, double aqueous phase extraction and layering are conducted in sequence, an upper phase is taken and put into a dialysis membrane of which the interception relative molecular mass is 10,000 to be dialysed for 15 h to 20 h, and a papain aqueous solution is obtained; freeze drying is conducted at -15 DEG C to -10 DEG C for 8 h to 15 h, and papain powder is obtained, wherein the average molecular weight of PEG in modified macrogol ester is 600 or 1,000 or 2,000. According to the method for conducting double aqueous phase extraction, separation and purification on the papain through modified polyethylene glycol-sodium tartrate, the selected double aqueous phase system is high in selectivity to the papain and high in system phase separation speed, phase separation can be conducted rapidly without the help of equipment such as a centrifugal machine, operation is easy and convenient, the equipment is conventional, the method is suitable for industrial production, and the obtained papain product has high purity and yield.