The invention discloses a modified sulfonated polyaryletherketone ion exchange membrane as well as a preparation method thereof. In the preparation process, reactions that keto group is reduced into hydroxy and hydroxy and sulfonic acid group are interlinked into sulphonate are generated in the sulfonated polyaryletherketone membrane, and a swelling-resisting cortical layer of a gradient structure is formed on each of two sides of the membrane. The preparation method comprises the following steps: soaking the sulfonated polyaryletherketone ion exchange membrane in a 0.025-2.5g/mL NaBH4 solution; washing with deionized water, and soaking in the deionized water; soaking the membrane in 0.01M-1.0M of an acid or alkaline solution; washing the membrane with deionized water, soaking and drying the membrane, thereby obtaining the surface modified sulfonated polyaryletherketone ion exchange membrane. The modified sulfonated polyaryletherketone ion exchange membrane as well as the preparation method thereof, which are provided by the invention, have the advantages that the modified method is simple; the process is simple and convenient to operate; the high conductivity of the membrane can be kept when the membrane is at the condition of certain size stability, mechanical intensity and fuel transmission resisting rate, so that the comprehensive performance of the membrane is improved greatly.