The invention relates to a method for separating lactoperoxidase from bovine whey and belongs to the technical field of biochemical engineering. According to the method, the bovine whey serves as a raw material liquid, cation exchange chimeric composite crystal gel with multistage pores serves as a separating medium, and conventional treatment, such as crystal gel chromatography, bed column balancing, sampling and adsorbing, buffer solution flushing, saliferous eluent stepwise elution, subsequent desalting and freeze drying, is carried out, so that high-purity lactoperoxidase with the purity of 98% is obtained through separating, and the yield can reach 92%. The cation exchange chimeric composite crystal gel medium has very good selectivity to lactoferrin and lactoperoxidase, which are difficultly separated through conventional chromatography, in the whey. The method has the advantages that steps are few, the operation is simple, the separation is rapid, the cost is low, and the obtained lactoperoxidase is high in purity and yield and has broad application prospects in the respects of high-value utilization of whey and separation of active protein.