Epitaxial growth of organized molecular films of alkylammonium-Au bis(1, 3-dithiole-2-thione-4, 5-dithiolate) ((dmit) 2 ) charge-transfer complex on fluorinated copolymer as template estimated by in-plane X-ray diffraction (XRD). In the single crystal, didodecylammonium-Au(dmit) 2 molecules packed triclinic lattice. From the in-plane XRD measurement of multilayers on hydrogenated solids, alkyl-chains of this complex also formed triclinic system. The orthorhombic packing of this complex film formed on fluorinated crystalline polymer as substrate. This structural transition is induced by crystal structure of fluorinated copolymer as template. On the other hand, disordered molecular arrangement in these two-dimensional films formed on the amorphous fluorinated copolymer.