A method is provided for purifying protein having steps of loading a sample containing proteins into a column containing an ion exchanger in a first direction to allow the ion exchanger to absorb proteins; and passing a salt solution through the column in a second direction opposite to the first direction to elute a target protein from the ion exchanger. The method is proven as capable of improving homogeneity of eluted target protein without combining minute and complicated techniques for protein purification. Therefore, the method is convenient, efficient and economic for purifying proteins.