Orientation-dependent ionization potentials (IPs) of organic thin films have been investigated with the combination of synchrotron-based high-resolution photoemission spectroscopy and near-edge X-ray absorption fine structure measurements. Organic thin films of copper(II)-phthalocyanine (CuPc) and its fully fluorinated counterpart of copper hexadecafluorophthalocyanine (F16CuPc with well-controlled orientation are used as model systems. Both molecules lie flat on the graphite surface and stand upright on Au(111) terminated by self-assembled monolayer of octane-1-thiol. The IP for the standing-up CuPc thin film (IP = 4.75 eV) is 0.40 eV lower than that of the lying-down film (IP = 5.15 eV). In contrast, the IP of the standing up F16CuPc (IP = 6.50 eV) is 0.85 eV higher than that of the lying-down film (IP = 5.65 eV). This reversed orientation dependence in IP is explained by the opposite surface dipoles in the standing-up CuPc and F16CuPc molecular layers originating from the different intramolecular dipolar bonds exposed at the surfaces, i.e., a net upward pointing Surface dipole in the standing-up CuPc thin film that lowers the IP, and a net downward pointing surface dipole in the standing-up F16CuPc thin film that increases the IP.