The invention provides a preparation method of a PCV2, PRRSV and mycoplasma hyopneumoniae triple inactivated vaccine. The technical scheme is that a brand-new preparation method is designed from culture, inactivation, complex and other levels based on growth characteristics of three microorganisms and physicochemical characteristics of an antigen substance. In the method, the PCV2 and the PRRSV are prepared by adopting a bioreactor mode; in the preparation process of an antigen, a pH value of fermented liquid is strictly controlled, so that the immunogenicity of a virus is effectively ensured;mycoplasam suis produces a strain in a bacteria fermenting tank; and in the breeding process of the strain, the homogenization of an intra-batch bacterial solution is ensured by setting dissolved oxygen, the pH value, rotating speed and the like, the defects of complex operation, high working intensity, easiness in pollution and the like in the rolling bottle culture process are eliminated, and the quality stability of the mycoplasam suis inactivated vaccine is effectively improved. Experiments show that the protection rates of the prepared triple inactivated vaccine for the PCV2, the PRRSV and the mycoplasma hyopneumoniae all exceed 80 percent, and preventing and treating demands on three pathogens are met.