A highly polar perovskite SrTiO3(STO) layer is considered as one of the promising artificial protective layers for the Zn metal anode of aqueous zinc-ion batteries (AZIBs). Although it has been reported that oxygen vacancies tend to promote Zn(II) ion migration in the STO layer and thereby effectively suppress Zn dendrite growth, there is still a lack of a basic understanding of the quantitative effects of oxygen vacancies on the diffusion characteristics of Zn(II) ions. In this regard, we comprehensively studied the structural features of charge imbalances caused by oxygen vacancies and how these charge imbalances affect the diffusion dynamics of Zn(II) ions by utilizing density functional theory and molecular dynamics simulations. It was found that the charge imbalances are typically localized close to vacancy sites and those Ti atoms that are closest to them, whereas differential charge densities close to Sr atoms are essentially non-existent. We also demonstrated that there is virtually no difference in structural stability between the different locations of oxygen vacancies by analyzing the electronic total energies of STO crystals with the different vacancy locations. As a result, although the structural aspects of charge distribution strongly rely on the relative vacancy locations within the STO crystal, Zn(II) diffusion characteristics stay almost consistent with changing vacancy locations. No preference for vacancy locations causes isotropic Zn(II) ion transport inside the STO layer, which subsequently inhibits the formation of Zn dendrites. Due to the promoted dynamics of Zn(II) ions induced by charge imbalance near the oxygen vacancies, the Zn(II) ion diffusivity in the STO layer monotonously increases with the increasing vacancy concentration ranging from 0% to 16%. However, the growth rate of Zn(II) ion diffusivity tends to slow down at relatively high vacancy concentrations as the imbalance points become saturated across the entire STO domain. The atomic-level understanding of the characteristics of Zn(II) ion diffusion demonstrated in this study is expected to contribute to developing new long-life anode systems for AZIBs.