Here, we develop a facile electrochemical polymerization method for the synthesis of polypyrrole (PPy) nanowires on Pd modified Nafion® membranes. Interestingly, with altering the deposition potential and temperature, we can easily tune the PPy nanowires from disordered nanostructures to well ordered vertically aligned nanowires. The various PPy nanowires show similar electronic conductivity but diverse hydrophobicity/hydrophilicity. The ordered PPy nanowires can significantly facilitate the mass transport and enhance the catalyst utilization. These two factors together make an obvious performance improvement of fuel cells.