The invention discloses an amphoteric ion exchange membrane for a fuel cell. The amphoteric ion exchange membrane employs polyvinyl alcohol and perfluorinated sulfonic acid resin as a membrane substrate, wherein negative ion exchange resin is intercalated into the membrane substrate in a particle mode, and nickel oxide hydroxide is loaded in the negative ion exchange resin particles. The invention also discloses a preparation method of the amphoteric ion exchange membrane. The preparation method comprises the steps of loading the nickel oxide hydroxide in the negative ion exchange resin particles, preparing gel of the membrane substrate comprising the polyvinyl alcohol and the perfluorinated sulfonic acid resin, forming the gel of the negative ion exchange resin intercalated into the membrane substrate in the particle mode, and further forming the amphoteric ion exchange membrane, wherein the additive proportion of the substrate membrane and the negative ion exchange resin is controlled by calculating positive ion conductivity s of the substrate membrane and negative ion conductivity s of the negative ion exchange resin particles during the preparation process. With the amphoteric ion exchange membrane prepared according to the method, the problems of low ion conductivity and fuel permeation of the negative ion exchange membrane are solved, and meanwhile, the problem that a proton exchange membrane shall employ precious metal as a catalyst is also solved.