The modulation of Schottky barrier height (SBH) due to defect migration has been suggested to be an important driving mechanism for resistive switching in metal-oxide-metal structures. Here, we explore the SBH and its modulation due to different interface structures and defects in the PtMgOPt(001) system using hybrid Heyd-Scuseria-Ernzerhof density functional theory. The computed magnitudes of SBH at PtMgO interfaces obtained using the generalized gradient approximation (local density approximation) functional are found to be significantly underestimated as compared to those obtained using hybrid functional. Furthermore, the magnitudes of SBH are found to depend critically on interface structures. In the case of defect-free PtMgO interfaces, the p-type SBH is found to be 4.13 eV and 3.04 eV for interfaces having adjacent Pt-O and Pt-Mg bonds, respectively. In addition, the SBH magnitudes are found to exhibit significant variation primarily due to nominal effective charges on interface layers which, in turn, are induced by interface defects such as O and Mg vacancies. The magnitudes of p-type SBH are found to increase (decrease) by ∼1.0-1.5 eV as the ionic layers with charge +1e (-1e) are introduced at the interface. The modulation in SBH due to interface ionic/polar layer is explained using a micro-capacitor model. Furthermore, the SBH is found to shift by ∼0.2 eV with the varying distance of O and/or Mg vacancies from the interface. Our results suggest that fluctuations in experimental resistive switching data in PtMgO structures may originate due to fluctuations in SBH induced by changes in interface atomic structure. The study also shows that SBH in PtMgO and related structures may be modulated in a controlled way by the insertion of interface polar layers. The lower and upper bounds of the SBH magnitudes are also estimated using a semi-empirical model expressed in terms of parameters such as charge neutrality level, ionization potential, pinning parameter, and metal work function. The quantitative results on the SBH modulation presented in the study may be expected to have important implications for resistive switching phenomenon in PtMgO and similar other structures. © 2020 Author(s).