In this study, a series of Cu–Ag–Se films were prepared on Si (100) substrate by magnetron sputtering. The phase composition, micro-structure and thermoelectric properties were studied. The results showed that the phase composition of deposited Cu–Ag–Se films varied from β-Cu2-xSe and a small amount of CuAgSe phase to majority β-Cu2-xSe and minority CuAgSe phase, minority β-Cu2-xSe and majority CuAgSe phase, CuAgSe and a small amount of β-Cu2-xSe phase, Ag2Se and a small amount of CuAgSe +β-Cu2-xSe phase as Ag content increased from 0.4 to 17.0, 20.8, 29.5, 41.4 at.%, respectively. In the deposited Cu–Ag–Se films, the carrier concentration first decreased and then increased and the mobility displayed an opposite trend with increasing CuAgSe content (decreasing β-Cu2-xSe content). The room temperature electrical conductivity and absolute value of room temperature Seebeck coefficient gradually increased with increasing CuAgSe content for the deposited Cu–Ag–Se films. The power factor of 29.5 at.% Ag samples (CuAgSe phase films) at whole measured temperature was the highest in all samples due to high Seebeck coefficient and high electrical conductivity, resulting in the highest PF value of 2.05 mW m−1 K−2 at 62 °C. However, due to its high thermal conductivity of 10.93 W m−1K−1, the room temperature ZT value of this sample was only 0.05 even if it possessed a higher PF value. Ag2Se phase films possessed the lowest PF value due to their lower Seebeck coefficient even if they possessed higher electrical conductivity.