Mg3Bi2/Mg2Sn nanocomposite films were prepared by high vacuum magetron sputtering with alternately sputtering on single crystalline Si substrate containing SiO2 layer of 500 nm thickness using high-purity Mg target and self-made Mg-Bi-Sn alloy target. The crystal structure and phase composition of the deposited films were determined by X-ray diffraction (XRD) patterns. The morphology and surface chemical composition of the deposited films were observed, measured and analyzed by field emission scanning electron microscopy (FESEM) and energy dispersive spectrum (EDS), respectively. The carrier concentration and mobility of the deposited films were obtained by Hall experiment. The electrical conductivity and Seebeck coefficient of the deposited films were measured by Seebeck/resistance measure and analysis system. The results show that the nanocomposite film is composed of Mg3Bi2 and Mg2Sn phase. Measurement and calculation of half height width of the diffraction peak for Mg2Sn phase show that the grain size of Mg2Sn phase in the deposited films is 13 nm to 16 nm. With the increase of Mg2Sn phase contents, the carrier concentration increases and the mobility decreases at room temperature. The phase interface is the barrier to carrier transmission, the carrier mobility decreases because of more phase interface. In the whole measured temperature range, the Seebeck coefficient increases and the conductivity decreases with the increase of Mg2Sn phase contents in the deposited film. The energy filtering effect at the phase interface causes carriers with lower energy to be filtered out, and the energy of carriers in the film is more concentrated, namely, the dp(E)/dE increases, causing Seebeck coefficient increases with the increase of phase interface. The film with 28.22% Mg2Sn atomic content of phase can obtain the highest power factor value of 1.2 mW·m-1·K-2 at 155 ℃. The power factor of Mg3Bi2 film can be significantly improved by adding proper amount of Mg2Sn second phase into Mg3Bi2 film, forming nanocomposite films.