This invention discloses a method for preparing recombinant diphtherin and its application. The recombinant diphtherin comprises diphtherin DAB389, a linker peptide (Gly4Ser) 2, and alpha-melanocyte stimulating hormone. The method comprises: (1) preparing a gene fragment of DAB389(Gly4Ser)2-alpha-MSH and a leading peptide, constructing an expression plasmid containing the gene fragment, and transforming Escherichia coli; (2) inducing with IPTG to obtain the target protein, purifying, digesting with Xa factor, and separating to obtain DAB389(Gly4Ser)2-alpha-MSH fusion protein. The method has such advantages as easy purification, and high yield. The recombinant diphtherin has high activity, and can attack and kill malignant melanoma without injuring normal cells, thus can be used to treat malignant melanoma.