Structure-related ionization energy (IE) of vacuum-deposited titanyl-phthalocyanine (OTiPc) thin films was investigated by using in situ ultraviolet photoelectron spectroscopy (UPS) and X-ray diffractometry. Distinct molecular orientations (i.e. lying-flat and standing-up orientation) in different polymorphous (i.e. monoclinic β-phase and triclinic α-phase) were observed on a surface of polycrystalline (poly-) Au and octadecyltrichlorosilane-self assembled monolayer (OTS-SAM). For the two structures IE of the highest occupied molecular orbital (HOMO) of OTiPc thin films altered significantly by 0.55 eV. The different IE was attributed to surface dipole potential and strong intermolecular interaction.