In this study, the effect of thickness of MgZnO thin films which provide high efficiency as photocatalyst under UV light on structural and photocatalytic performance was investigated. For this reason, MgZnO thin films were produced by RF/DC magnetron sputtering technique at room temperature. MgZnO thin films at different thicknesses were deposited on Si (100) substrate and samples were subsequently annealed in the oven at 400 °C for 1 hour. Structural and morphological properties of MgZnO thin films were investigated using the Scanning Electron Microscopy (SEM), Grazing Incident X-ray diffraction (GIXRD) and Atomic Force Microscopy (AFM). All films have hexagonal-wurtzite crystal structure. Also, the crystallite size was 22.95 nm for the 400 nm film and the average crystallite size rised to 35.42 nm with increasing film thickness. The results showed that the structural properties roughness and surface morphology of the films varied depending on the thickness. Also, photocatalytic performances of MgZnO thin films at different thicknesses were measured by UV–Vis spectroscopy. The reaction rate constant (k) for MgZnO photocatalyst with a thickness of 800 nm was calculated as 27.86x10-2s-1. This result shows that photocatalysts of different thickness suitable with the first-order velocity law because the thin films degradation in the low concentration methylene blue (MB) solution.