A new π-conjugated polymer based on naphthalenediimide with a branched semifluoroalkyl side chain (FNDIT2) was synthesized and used to change the polymer orientations in thin films. X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy revealed that FNDIT2 spontaneously forms surface-segregated monolayers in blend films with other π-conjugated polymers to adopt a preferred face-on orientation, with the π-plane of the polymer aligned more parallel to the surface. Thermal annealing of the films induced further reorientation of the polymers inside the films closer to the face-on orientation, as shown by two-dimensional grazing-incidence wide-angle X-ray scattering. The induced face-on orientations in the films led to higher charge mobility in the vertical direction. This study provides a general and versatile strategy to control the molecular orientation in thin films and enhance the performance of thin-film organic electronics.