The invention relates to a method for purifying papain with a metal affinity membrane, which comprises the steps that (1) a nylon membrane is activated with formaldehyde and modified with chitosan; (2) the activated and modified nylon membrane reacts with the mixture solution of epichlorohydrin, sodium hydroxide and sodium borohydride; and the membrane is submersed in the mixture solution of sodium carbonate, sodium borohydride and an coupling agent, and in copper sulphate solution, respectively to get the chelating copper ion metal affinity membrane; (3) the metal affinity membrane is foldedup to become a membrane pile, and the membrane pile is arranged in a membrane bridge before the membrane pile is fed into Tris-HCl buffer solution and eluent with a peristaltic pump; subsequently, the membrane pile is fed into papain solution, and is eluted with the eluent, thus getting the target product, namely papain; (4) the enzyme activity and the protein content are tested, and purificationfactor is calculated. The method is quick, simple and convenient, and can be used for separating papain in large quantity, and is applicable for large-scale production. In addition, the activity of the extracted enzyme is excellent.