Thin films of zinc titanate (ZnTiO3) can be produced on Si(100) substrates at room temperature by DC reactive magnetron co-sputtering with Ti, Zn as the target and O2 as a reactive gas. In this work, the influence of annealing temperature (500–900 °C) on microstructure and formation of ZnTiO3 thin films were investigated. The samples are characterized by X-ray diffraction, transmission electron microscopy, scanning electron microscopy, atomic force microscopy, electron spectroscopy for chemical analysis. As-deposited films have an amorphous columnar structure. The crystallization phenomenon was observed with annealing temperature of 500 °C. After 600 °C 2 h annealing, crystalline phase with ZnTiO3 (hexagonal) and TiO2 (rutile) could be obtained and coexisted. Furthermore, the unit cell size of the ZnTiO3 and TiO2 crystal is a = ~5.062 Å, c = ~ 13.87 Å and a = ~4.58 Å, c = ~ 2.95 Å.