The effects of substrate temperature on the microstructure and morphology of CdZnTe thin films were investigated in detail. The CdZnTe thin films were deposited on glass substrates at 200°C, 300°C and 400°C by radio frequency magnetron sputtering and annealed at 450°C for an hour under N2 ambient at atmospheric pressure. The microstructure and morphology of the CdZnTe films were analyzed by using x-ray diffractometry, scanning electron microscopy, energy dispersive x-ray spectroscopy and atomic force microscopy. The effects of substrate temperature on transmission spectra of the CdZnTe films were also investigated. The experimental results show that the optimum morphology and crystalline thin film structures were achieved at 400°C growth temperature. At higher substrate temperatures, atomic mobility and diffusion are promoted, which can stabilize the uniformity and crystallite size. The crystalline grains enlarge and the surface morphology becomes smoother due to growth of grains in the CdZnTe thin films. In addition, the transmission spectra of the films are consistent with the morphological changes. It may be concluded that substrate temperature in growing CdZnTe films has a substantial effect on morphological characteristics, and desired quality of the CdZnTe thin films may be fabricated at higher substrate temperatures.