In this paper, molybdenum (Mo) thin films are deposited on soda-lime glass (SLG) substrates by direct current magnetron sputtering and heated in three different modes at different temperatures, including substrate heating, annealing treatment, and both substrate heating and annealing treatment. The effects of heating temperature and heating mode on the structures, morphology, optical and electrical properties of Mo thin films were systematically investigated by X-ray diffraction (XRD), Scanning electron microscopy (SEM), atomic force microscope (AFM) and UV-visible spectrophotometer (UV-vis spectra). It is shown that as the substrate and annealing temperature increase, the crystallinity of Mo thin films is improved, and the grain sizes become bigger. Especially in the mode of both substrate heating and annealing treatment at higher temperature, the obtained Mo thin films show higher crystallinity and conductivity. Moreover, with the increase of substrate and annealing temperature in different heating modes, both the surface compactness of Mo films and the optical reflectance increase correspondingly. Furthermore, the Mo film, prepared at the substrate heating temperature of 400 °C and annealed at 400 °C, showed excellent comprehensive performance, and the resistivity is as low as 1.36 × 10−5 Ω·cm. Using this optimized Mo thin film as an electrode, copper indium gallium selenium (CIGS) solar cells have a maximum photo-conversion efficiency of 12.8%.