The invention discloses a sulphonated naphthalene ether grafted fluorinated polyether containing proton exchange membrane and a preparation method thereof. The proton exchange membrane is synthesized through the following steps that 1, a polyether polymer containing perfluoro-substitution benzene rings is synthesized through a nucleophilic substitution reaction; 2, a bis-sulfonated naphthalene ether grafted fluorinated polyether containing polymer is synthesized through the nucleophilic substitution reaction between bis-sulfonated naphthol and the perfluoro-substitution benzene rings; 3, the obtained polymer is dissolved in an organic solvent according to a certain proportion, and the membrane is formed through a solution casting method. A series of bis-sulfonated naphthalene ether grafted fluorinated polyether containing polymers with the ion exchange capacity are synthesized by changing the proportion of bis-sulfonated naphthol and the fluorinated polyether containing polymer, the synthesis process is simple, the degree of sulfonation can be controlled, the reactivity and hydrophobicity of Aromatic substitution fluorine atoms are utilized, and the prepared proton exchange membrane is moderate in water absorption, excellent in dimension stability, good in chemical stability and high in conductivity.