Oxygen defects are usually unavoidable when synthesizing oxide thin films. We study the origin of the oxygen defects in hexagonal manganite HoMnO 3 epitaxial thin films through Raman scattering spectroscopy. Our results show that the oxygen defects in hexagonal HoMnO3 thin films have distinct effects on different phonon modes and on magnon scattering. Our analyses indicate that the oxygen defects in hexagonal HoMnO3 thin films mainly originate from the basal O3 and/or O4 oxygen vacancies. Furthermore, our analyses of oxygen defects predict that the Mn 3d orbitals would be more strongly hybridized with the apical O1 and/or O2 2p orbitals than the basal O3 and/or O4 2p orbitals. This prediction is consistent with our resonant Raman scattering study and earlier first-principle calculations of the electronic structures of hexagonal manganites.