Poly(3,4-ethylenedioxythiophene) (PEDOT) films doped with nitric and chlorine ions have been electrochemically deposited simply by a one-step electrochemical method in an aqueous media in the absence of any surfactant. The fabricated PEDOT films were characterized by scanning electron microscopy, transmission electron microscopy, and Raman spectroscopy. The results indicate that the hierarchical structured PEDOT film doped with nitric ions displays a 'lunar craters' porous morphology consisting of PEDOT nano-sheets with a thickness of less than 2 nm. The effect of counter ions on the electro-polymerization, the electrochemistry, and the morphology of the polymer film was studied. Compared with PEDOT film doped with nitric acid, PEDOT film deposited in the presence of chlorine ions shows irregular morphology and less electrochemical activity. The specific nanostructure of the polymer was further studied as catalyst support for platinum nanoparticles to methanol electro-oxidation.