Defects can influence the properties of photocatalysts, and defective ZnO has triggered broad interest and intensive studies for decades. However, the correlation between crystal planes and defects remains unclear. Here, we demonstrate that the (101) plane is superior in producing oxygen vacancies than the (100) plane in rod-like defective ZnO samples. While the optimum intensity of the crystal ratio, (101)/(100), approaches 1, the separation efficiency of electrons-holes is much enhanced. Furthermore, it is found that the (101) plane has stronger spontaneous adsorption and higher dissociation activity of H2O, which is conducive to the spontaneous formation of oxygen vacancies and eventually enhances the separation efficiency of electrons-holes. The charge difference also shows that the crystal boundary junctions could cause uneven charge distribution, inducing lattice polarization and boosting the charge separation of defective ZnO, which is helpful for improving the photocatalytic activities. As a new proposed mechanism, the relationship between defect engineering and crystal surface could provide inspiration for the design of special nanomaterials for the environment purification and energy fields.