[Background] The future development of pertussis vaccine is acellular pertussis (component) vaccine, which could significantly reduce the incidence of adverse events after inoculation. This new type of vaccine needs to remove the endotoxin in the process of production. [Objective] In our study, the removal process of the endotoxin from pertussis filamentous hemagglutinin (FHA) was investigated by optimized chromatography purification with response surface methodology. [Methods] The process of chromatographic purification was verified by the single factor experiment, to ensure the range of response surface methodology; the method of response surface analysis was adopted according to the CCD experimental design principles by using Minitab software: the variable factors were pH, Cond, and Mass; Response values were considered the concentration of FHA protein and recovery of FHA, and finally combined the value of endotoxin. [Results] These results showed that the optimum conditions for chromatographic process of endotoxin removal from pertussis filamentous hemagglutinin were as follows: pH 5.3, Cond 9.6, and Mass 3.0. [Conclusion] The optimum processes of chromatographic purification on endotoxin removal were screened successfully by response surface methodology. This method has advantages of higher efficient and lower energy consumption, which will lay a good foundation for the subsequent biological process of expanded reproduction.