The impact of intramolecular polar bonds (IPBs) on the energy level alignment in layered systems of rodlike conjugated molecules standing on the substrate was investigated for pentacene (PEN) and perfluoropentacene (PFP) on SiO(2) using ultraviolet photoelectron spectroscopy. A remarkably large energy offset of 1.75 eV was found between the highest occupied molecular orbital (HOMO) levels of PEN and PFP caused by IPBs at the surface of standing PFP layers. This large HOMO-level offset results in a narrow intermolecular energy gap of approximately 0.4 eV at the interface between PEN and PFP layers. However, the absence of significant spatial overlap of PEN and PFP electron wave functions across the layers suppresses interlayer optical transitions.