Molecular alignment at the interface between the electron donor and acceptor (D/A) materials in thin films may have a large effect on the charge generation process in organic solar cells (OSCs). In this study, the effects of the polymer chain orientations at the D/A interface were investigated in OSCs with planar heterojunction (PHJ) structures. Poly(3-alkylthiophene) films with edge-on (main chain parallel to the interface) and end-on (main chain vertical to the interface) orientations at the surface were used to construct PHJs with a fullerene derivative. Ultraviolet photoelectron spectroscopy and low-energy inverse photoelectron spectroscopy revealed that the difference in polarization energy through the charge-permanent quadrupole interaction causes a rigid energy shift of 0.5 eV between the two orientations. The PHJ device with the end-on oriented polymer chains at the D/A interface showed a smaller photovoltage loss expected from the energy structure and a more efficient charge separation than the device with the edge-on oriented polymer chains. These improvements were attributed to charge delocalization along the end-on oriented polymer chains normal to the D/A interface, through which the effective binding energy of the charge pairs in the interfacial charge-transfer state was reduced. These results provide important information about molecular arrangements at the D/A interface that may enable further improvements in OSC performance.