Crystal growth and fluorescent characteristics of a quinoline-capped thiophene oligomer were investigated in thin films grown on the (001) surface of KCl by a hot-wall epitaxy technique. Under controlled substrate and wall temperatures, the deposited film consisted of two types of crystallites: one was epitaxial needles oriented along the (100)(KCl) and (110)(KCl) directions, and another was irregular aggregates among them. Fluorescence spectromicroscopy revealed that the former crystals exhibited a red-shifted emission band with respect to the latter. Microscopic Raman spectra for the individual crystallites and vibrational analysis by molecular orbital calculations identified the origin of this fluorescence difference as cis-trans isomerization of the peripheral quinoline groups. In the epitaxial needles, the trans-form molecules were lying parallel to the KCl surface while in the irregular aggregates the cis-form molecules were standing. The detailed crystallization depending on the isomerization was also supported by scanning near-field/confocal scanning laser and transmission electron microscopies.