In situ synchrotron-based near-edge x-ray absorption fine structure measurements and photoemission spectroscopy have been used to investigate the effect of molecular orientation on the interfacial dipole and the energy level alignment at the interfaces of organic heterojunctions comprising copper-hexadecafluoro-phthalocyanine ( F ₁₆ Cu Pc ) on both standing-up and lying-down copper(II) phthalocyanine (CuPc) thin films. It is found that F ₁₆ Cu Pc thin films adopt the same molecular orientation of the underlying CuPc thin films. An interfacial dipole of 0.45 eV forms at the interface of lying-down F ₁₆ Cu Pc / Cu Pc on highly ordered pyrolytic graphite. In contrast, a much larger interfacial dipole of 1.35 eV appears at the interface of standing-up F ₁₆ Cu Pc / Cu Pc on octane-1-thiol terminated Au(111).