A poly(3-dodecylthiophene-2,5-diyl) film having in-plane anisotropic molecular arrangement was successfully fabricated by transferring its Langmuir-Blodgett film onto a step-bunched Si(111) substrate. Polarized near-edge X-ray absorption fine structure measurements revealed that the polythiophene main chains are preferentially orientated along periodic facet/terrace nanostructures on the step-bunched substrate, whereas less anisotropy was found on a flat substrate. The step-bunched Si substrate has been proved to be effective for controlling the in-plane molecular arrangement in the polymer thin film.