The invention provides a method for purifying a foot-and-mouth disease virus antigen by utilizing ion-exchange chromatography, which comprises the following steps: inactivating and filtering a harvested foot-and-mouth disease virus solution, and sequentially carrying out PEG (Polyethylene Glycol) precipitation, redissolution, ion-exchange chromatography and the like. Wherein the ion exchange chromatography comprises the following steps: adopting a flow-through process, enabling a redissolved solution to pass through a chromatographic column, and collecting a flow-through component. By adopting the process, the yield of three subtype inactivated antigens of foot-and-mouth disease AKT-III, O/Mya 98 and OHM02 is more than 90%, the purity is more than 70%, the content of impure protein in the antigens is greatly reduced, more than 50% of total protein can be removed, the process is stable in amplification and short in time consumption, the process can be used for preparing high-quality foot-and-mouth disease vaccines, and the safety and effectiveness of the foot-and-mouth disease vaccines are improved.