The invention discloses a method for purifying oxidized beta-nicotinamide adenine dinucleotide phosphate. The method for purifying oxidized beta-nicotinamide adenine dinucleotide phosphate concretely comprises the following steps: a, successively carrying out microfiltration and nanofiltration on a pretreated coenzyme II solution by adopting membrane concentration equipment, so that a concentrated crude product solution is obtained; b, regulating the pH value of the obtained crude product solution to 2-4, injecting a sample, loading the sample onto a reversed high performance liquid chromatography preparation column, carrying out gradient elution, and purifying, so that a purified sample solution is obtained; and c, carrying out nanofiltration on the purified sample solution by adopting the membrane concentration equipment, and freeze-drying by adopting a vacuum freeze-drying machine, so that purified coenzyme II is obtained. The coenzyme II prepared by adopting the method disclosed by the invention is high in purity, and the yield is high, so that the method disclosed by the invention has a good market prospect.