The present application relates to a method for preparing a foot-and-mouth disease (FMD) vaccine, comprising the following steps: (i) obtaining cell culture media containing FMD virus; (ii) separating and purifying the cell culture media containing FMD virus by an integrated filtration system with two membranes in combination; and (iii) collecting the concentrated solution containing FMD virus obtained in step (ii). The present application also relates to an FMD vaccine prepared by the method described herein and use thereof in the manufacture of a medicament for preventing animal FMD. The present application further relates to an apparatus for preparing an FMD vaccine, which comprises an integrated filtration system with two membranes in combination.