The invention provides a preparation method of a binary inactivated vaccine against a Japanese encephalitis virus and a porcine parvovirus, which comprises the following steps of: (1) inoculating the animal cells to a microcarrier for performing the absorption culture and multiplication culture processes of the cells in a tidal biological reactor; (2) inoculating the Japanese encephalitis virus and the porcine parvovirus on the cells being subjected to multiplication culture; (3) when the inoculated animal cell CPE (Cytopathic Effect) reaches above 75%, harvesting a viral solution; and (4) freezing and thawing the harvested viral solution twice at minus 20 DEG C, inactivating after the concentration, and adding an emulsifier for emulsification to obtain the binary inactivated vaccine against Japanese encephalitis virus and porcine parvovirus. The binary inactivated vaccine provided by the invention has the advantages of good immunogenicity, stable growth and high titer of the preserved seed virus; and the tidal biological reactor is adopted to respectively culture and harvest two viruses with high titers, and the two viruses are directly emulsified and prepared after the concentration and the inactivation, so that the binary inactivated vaccine can be continuously produced in a large scale.