Forming heterostructures based on hybrid photocatalysts has been considered as one of the most effective techniques for improving the photocatalytic efficacy of semiconductor photocatalysts. To address this issue, this article describes ZnO/TiO₂ heterojunction thin films that were produced via the direct current reaction magnetron sputtering technique and with varying thickness of TiO₂ coating. The structural, morphological, and optical features were thoroughly characterized by X-ray diffraction, scanning electron microscope, photoluminescence, and ultra-violet-visible transmission spectra. The photocatalytic and antibacterial ability were assessed by the photo-degradation of methyl orange (MO) aqueous solution and count method of E. coli bacteria. The results demonstrated that the photocatalytic and antimicrobial efficacy of the ZnO/TiO₂ heterojunction was found to vary depending on the morphology of the TiO₂ layer. In addition, their photocatalytic (91% MO degradation within 150 min) and antimicrobial efficacy (92.7% antibacterial efficiency within 90 min) were higher than the efficiency of either material alone. This could can be ascribed to the photogenerated charge carrier efficiency and hierarchical nanostructure with a large surface area. The mechanism for the improved photocatalytic performance has been discussed in detail.