Photocatalytic degradation of organic pollutants in water is a highly efficient and green approach. However, the low quantum efficiency is an intractable obstacle to lower the photocatalytic efficiency of photocatalysts. Herein, the TiO₂/ZnO heterojunction thin films combined with surface oxygen vacancies (OVs) were prepared through magnetron sputtering, which was designed to drive rapid bulk and surface separation of charge carriers. The morphology and structural and compositional properties of films were investigated via different techniques such as SEM, XRD, Raman, AFM, and XPS. It has been found that by controlling the O₂/Ar ratio, the surface morphology, thickness, chemical composition, and crystal structure can be regulated, ultimately enhancing the photocatalytic performance of the TiO₂/ZnO heterostructures. In addition, the heterojunction thin film showed improved photocatalytic properties compared with the other nano-films when the outer TiO₂ layer was prepared at an O₂/Ar ratio of 10:35. It degraded 88.0% of Rhodamine B (RhB) in 90 min and 90.8% of RhB in 120 min. This was attributed to the heterojunction interface and surface OVs, which accelerated the separation of electron–hole (e–h) pairs.