Understanding the influence of adsorption sites to the electronic properties of adsorbed molecules on two-dimensional (2D) ultrathin insulator is of essential importance for future organic-inorganic hybrid nanodevices. Here, the adsorption and electronic states of manganese phthalocyanine (MnPc) on a single layer of hexagonal boron nitride (h-BN) have been comprehensively studied by low-temperature scanning tunneling microscopy/spectroscopy and tight binding calculations. The frontier orbitals of the MnPc can change drastically by reversible manipulation of individual MnPc molecules onto and away from the single atomic vacancies at the h-BN surface. Particularly, the change of the molecular electronic configuration can be controlled depending on whether the atomic vacancy is below the metal center or the ligand of the MnPc. These findings give new insight into defect-engineering of the organic-inorganic hybrid nanodevices down to submolecular level.