The invention belongs to the technical field of high polymer materials and relates to a side-chain sulfonic acid type polyarylether polymer which has high thermal stability and is used in a proton exchange membrane of a fuel cell and a preparation method thereof. The preparation method comprises the following steps: adding a diphenol monomer, a sulfonated difluoro-monomer, a difluoro-monomer and anhydrous potassium carbonate in a three-necked bottle provided with a stirrer, a water-carrying device and a nitrogen hole, adding a solvent and an azeotropic dehydrant which accounts for 20% of the solvent by volume in the three-necked bottle, injecting nitrogen, and heating to reflux the azeotropic dehydrant; and refluxing for 2-5h to dehydrate, evaporating the azeotropic dehydrant, heating to 175-190 DEG C to react for 5-8h, then pouring the reaction mixture in water to obtain a polymer, grinding the polymer to fine particles by using a grinder, filtering by using a buchner funnel, washingwith deionized water and ethanol several times, and performing vacuum drying at 100-110 DEG C for 10-15h to obtain the side-chain sulfonic acid type polyarylether polymer with high thermal stability,good solubility and film-forming property and low water absorption rate.