In this work, we reported a comparative study of ZnO thin films grown on quartz glass and sapphire (001) substrates through magnetron sputtering and high-temperature annealing. Firstly, the ZnO thin films were deposited on the quartz glass and sapphire (001) substrates in the same conditions by magnetron sputtering. Afterwards, the sputtered ZnO thin films underwent an annealing process at 600 °C for 1 h in an air atmosphere to improve the quality of the films. X-ray diffraction, scanning electron microscopy, atomic force microscopy, X-ray photoelectron spectroscopy (XPS), ultraviolet-visible spectra, photoluminescence spectra, and Raman spectra were used to investigate the structural, morphological, electrical, and optical properties of the both as-received ZnO thin films. The ZnO thin films grown on the quartz glass substrates possess a full width of half maximum value of 0.271° for the (002) plane, a surface root mean square value of 0.50 nm and O vacancies/defects of 4.40% in the total XPS O 1s peak. The comparative investigation reveals that the whole properties of the ZnO thin films grown on the quartz glass substrates are comparable to those grown on the sapphire (001) substrates. Consequently, ZnO thin films with high quality grown on the quartz glass substrates can be achieved by means of magnetron sputtering and high-temperature annealing at 600 °C.