The invention relates to a zwitter Nafion ion exchange membrane for vanadium batteries and a preparation method thereof. Commercial perfluorosulfonic acid Nafion or Nafion resin is taken as the initiator; and through atom transfer radical polymerization (ATRP) reactions, different cationic or anionic polymers are grafted to the surface or body of a Nafion membrane so as to improve the ion selectivity of Nafion when Nafion is applied to an all-vanadium redox flow battery without influencing the conductivity of Nafion. The obtained Nafion zwitter ion membrane has the advantages of a Nafion membrane such as excellent proton conductivity, chemical stability, and the like, and moreover, the ion selectivity of the Nafion membrane is improved effectively. By adjusting the kinds and ratios of cationic and anionic polymerization monomers, the structure and performance of prepared Nafion zwitter membrane can be adjusted conveniently. The operation is simple, the reaction conditions are mild, thegrafting amount is controllable, large scale production can be realized conveniently, and the commercial prospect is very good.