We used aromatic phosphonates with substituted phenyl rings with different molecular dipole moments to form self-assembled monolayers (SAMs) on the Zn-terminated ZnO(0001) surface in order to engineer the energy level alignment at hybrid inorganic/organic semiconductor interfaces, with an oligophenylene as organic component. The work function of ZnO was tuned over a wide range of more than 1.7 eV by different SAMs. The difference in the morphology and polarity of the SAM-modified ZnO surfaces led to different oligophenylene orientation, which resulted in an orientation-dependent ionization energy that varied by 0.7 eV. The interplay of SAM-induced work function modification and oligophenylene orientation changes allowed tuning of the offsets between the molecular frontier energy levels and the semiconductor band edges over a wide range. Our results demonstrate the versatile use of appropriate SAMs to tune the energy levels of ZnO-based hybrid semiconductor heterojunctions, which is important to optimize its function, e.g., targeting either interfacial energy- or charge-transfer.