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Film thickness is very important in the preparation of film thermoelectric (TE) devices. To define the effect of the film thickness on the power factor and output power, the ZnO:Al films with thicknesses in the range of 100 nm–900 nm were prepared by thermal evaporation method assisted by radio frequency atomic source. The results show that the film thickness has no effect on the phase composition and the (002) preferred orientation of the wurtzite phase in the films. However, the grain size, surface particle size, and surface roughness increase with increasing film thickness. Transmittance significantly reduced for the 900 nm film. Meanwhile, the film thickness affects the carrier concentration and mobility through the defects and growth modes, so that the TE parameters of the films change with the film thickness. The 700 nm film has the highest power factor, and the maximum power factor is 627 μW m−1 K−2 at 560 K. The output power of the films increases as the increase of the temperature on the hot side and higher power factor results in higher output power. The maximum output power of the 700 nm film is 116.01 pW at temperature difference of 1 K. This indicates that film thickness, temperature difference, and power factor are the key factors affecting the film output power. [ABSTRACT FROM AUTHOR]