The invention discloses a method for separating and purifying whooping cough toxins and filamentous hemagglutinin. The method comprises the following steps: S1, performing sample treatment, namely ending culture of bordetella pertussis, removing the thallus, collecting the supernatant, and concentrating the supernatant by using an ultrafiltration membrane; S2, performing primary chromatography comprising the sub-steps of eluting hybrid proteins, separating the whooping cough toxins and separating and purifying the filamentous hemagglutinin; and S3, performing secondary chromatography, namely loading a coarse product of the separated whooping cough toxins onto a CaptoMMC chromatographic column, eluting the buffer solution, collecting the eluant at the OD280 elution peak, thereby obtaining the purified whooping cough toxins. With the adoption of the CaptoSPImpRes chromatographic column and the CaptoMMC chromatographic column, the supernatant of the bordetella pertussis culture solution is separated and purified, so that PT and FHA can be accurately obtained, the quality is controllable, the purity of the separated and purified whooping cough antigen proteins is over 95 percent, and the method has the advantages of simplicity in operation, high purification speed and low cost.