The invention relates to a method for preparing a multilayer filler/fluoroether rubber composition through a layering method. The method includes the steps that filler such as carbon black and carbon nanotubes is dispersed on the surfaces of rubber thin films through a direct dispersion method or jet dispersion method; and the rubber thin films containing the filler are compounded layer by layer and then pressurized and vulcanized to obtain a fluoroether rubber material with a multilayer structure. According to the method, the filler/fluoroether rubber composition which is prepared by compounding a single-filler network structure into the multilayer structure with different dimensions or distribution characteristics through a special process method brings excellent performance in all directions into play, has excellent tensile strength, elongation at break and medium resistance, is suitable for being used in sealed environments, and further improves reliability of sealing structures.