The control of native defects in the ZnO material is strongly important for a wide range of technological applications. In this paper, native defects are tuned via the post-thermal treatment of ZnO films in a high vacuum atmosphere. The microstructure of the as-grown ZnO film shows columnar growth and strongly polar-oriented grains along the c-plane (002). Also, the obtained results indicate that the as-grown film contains a high amount of intrinsic defects and strong lattice distortions. After the thermal annealing, the ZnO films display significant structural changes, which are reflected in their electrical, vibrational, and optical properties. Our findings suggest that these changes were attributed to the selective cleanup effect of the native defects and the partial deoxidation process mainly on the exposed particle surface (at high temperatures) tuned up by the thermal annealing temperature. According to DFT calculations, oxygen vacancies (V O ) show lower energy, followed by zinc vacancies (V Zn ) and oxygen interstitials (O i ) indicating that V O defect is the most stable in ZnO. That sequence of stability could suggest the sequence of the annihilation of those defects, which is in line with our experimental findings and also in agreement with literature results.