Structure-dependent electrochromism was investigated with vapor-deposited thin films of zinc and vanadyl naphthalocyanines (ZnNc and VONc). The amorphous ZnNc film deposited on an indium tin oxide (ITO) coated glass electrode exhibited an irreversible electrochromic oxidation in 0.1 M KCl. This reaction gave rise to swelling of the film surface due to expansion of grains caused by incorporation of charge-compensating anions between the aggregated molecules. Epitaxially oriented films were prepared by deposition onto the (001) cleavage surface of NaCl and then transferred onto the ITO electrode. The epitaxial ZnNc film, in which the planar molecules are piled up in columns taking on the face-to-face, eclipsed stacking, exhibited both electrochromic reduction and oxidation. This electrochromic activity was attributed to a reversible incorporation of counterions through hollow channels between the molecular columns, which was accompanied with rearrangement in the molecular stacking. By contrast, no electrochromic reaction occurred for the epitaxial VONc film, where the alternately slipped dimeric structure did not facilitate a penetration of counterions into the stacked molecules.