High quality In-doped ZnO (ZnO:In) thin films were deposited on the quartz glass substrates at room temperature by using radio frequency magnetron sputtering. The effect of annealing temperature on the structure and optical properties of the ZnO:In films was investigated. It was found that the as-deposited film has a hexagonal wurtzite structure with c-axis perpendicular to the substrate. Accompanying with increasing annealing temperature from 400 °C to 700 °C, the crystal quality of the thin films can be improved, and then it will be deteriorated when the annealing temperature goes over 700 °C. The transmittance of the ZnO:In films was revealed to be 85% in the visible region, and it changes slightly after annealing. The optical band gap increases from 3.17 eV to 3.23 eV with annealing temperature due to the decrease of the tensile strain in the films, and a linear relationship between the band gap and the strain was obtained. PL results show that all the emissions increase while annealing temperature rising from 400 °C to 800 °C and the origins of all the emissions were discussed in detail.