Taking Mg2Si sintered target as target, Mg2Si amorphous thin films were deposited on Si, quartz and Al2O3 substrates by magnetron sputtering method, and then the effects of substrate type, annealing temperature and annealing time on the structure of Mg2Si polycrystalline thin films were investigated. The results show that the optimal annealing temperature and annealing time of Mg2Si films on Si, quartz and Al2O3 substrates are all 350 °C and 1 h. The crystal quality of Mg2Si film on the Al2O3 substrate is the best, followed by that on Si substrate, and that on quartz substrate is the worst. And it is found that this difference is mainly due to the different thermal mismatch between the substrate and the film.