A bilayer complex proton exchange membrane and a membrane electrode assembly are provided. The bilayer complex proton exchange membrane includes a first complex structure and a second complex structure. The first complex structure includes 0.001-10 wt % of a graphene derivative with two dimension configuration, and 99.999-90 wt % of organic material. The organic material includes polymer material having sulfonic acid group or phosphate group. The second complex structure includes 0.5-30 wt % of inorganic material and 99.5-70 wt % of organic material, wherein a surface area of the inorganic material is 50-3000 m2/g, and the organic material includes polymer material with sulfonic acid group or phosphate group.