Bismuth telluride films were prepared on the quartz glass by magnetron sputtering at various temperatures. Co-sputtering method with the alloying Bi2Te3 and Te targets was adopted to adjust the content of Te. The influence of Te content and deposition temperature on microstructure and thermoelectric performance was investigated systematically. Irregular hexagonal grains were observed in the surface of films prepared at 300 °C, but part of irregular hexagonal grains became to triangular and truncated triangular morphology with layered structure at elevated temperature when only one alloying Bi2Te3 target was used. However, lamellar grains could be observed at 300 °C and 350 °C particularly when films were prepared by the alloying Bi2Te3 and Te targets, which indicated that Te content had an obvious effect on surface morphology. In addition, the Seebeck coefficient and power factor of films which prepared by co-sputtering increased, compared with the films prepared at the same temperature only by the alloying Bi2Te3 target. And the Seebeck coefficient and power factor of films were higher with increase of deposition temperature. Maximum Seebeck coefficient and power factor of bismuth telluride films have been prepared at 400 °C by the alloying Bi2Te3 and Te targets, which attributed to the optimum of Te content and deposition temperature.