A simple method was developed to prepare ultra-low Pt loading membrane electrode assembly (MEA) using vertically aligned carbon nanotubes (VACNTs) as highly ordered catalyst support for PEM fuel cells application. In the method, VACNTs were directly grown on the cheap household aluminum foil by plasma enhanced chemical vapor deposition (PECVD), using Fe/Co bimetallic catalyst. By depositing a Pt thin layer on VACNTs/Al and subsequent hot pressing, Pt/VACNTs can be 100% transferred from Al foil onto polymer electrolyte membrane for the fabrication of MEA. The whole transfer process does not need any chemical removal and destroy membrane. The PEM fuel cell with the MEA fabricated using this method showed an excellent performance with ultra-low Pt loading down to 35 μg cm−2 which was comparable to that of the commercial Pt catalyst on carbon powder with 400 μg cm−2. To the best of our knowledge, for the first time, we identified that it is possible to substantially reduce the Pt loading one order by application of order-structured electrode based on VACNTs as Pt catalysts support, compared with the traditional random electrode at a comparable performance through experimental and mathematical methods.