The invention provides a hydrophilic fluorinated polymer with a sulphonate side group, which is prepared by performing multi-component copolymerization on tetrafluoroethylene and two types of sulphonate side group vinyl ether monomers with different structures. A perfluorinated ion exchange membrane prepared by the assistance of the fluorinated polymer not only has resistance to various chemical mediums, but also has high electrical conductivity, high mechanical intensity, high size stability, low membrane resistance and long service life, and is suitable to be used in a fuel cell or a chlorine-alkali electrolytic cell. The invention also provides a preparation method and application of the hydrophilic fluorinated polymer.