Zinc oxide thin films deposited on glass substrate at 150 °C by atomic layer deposition were annealed by the microwave method at temperatures below 500 °C. The microwave annealing effects on the structural and luminescent properties of ZnO films have been investigated by X-ray diffraction and photoluminescence. The results show that the MWA process can increase the crystal quality of ZnO thin films with a lower annealing temperature than RTA and relatively decrease the green luminescence of ZnO films. The observed changes have demonstrated that MWA is a viable technique for improving the crystalline quality of ZnO thin film on glass.