The thermoelectric properties of In−Sn−O (ITO) thin films were estimated in relation to microstructures with various zinc concentrations. The zinc-doped ITO (ITO:Zn) thin films were amorphized with increasing zinc concentration. The carrier density (n) of the thin films decreased as the zinc content increased, which could be attributed to a decline in oxygen vacancies. The highest Seebeck coefficient (S, 64.91 μV/K) was obtained with an ITO film containing 15.33 at.% of Zn due to the low n value, which also exhibited the highest power factor (234.03 μW K−2 m−1). However, the highest thermoelectric figure of merit value (0.0627) was obtained from the film containing 18.26 at.% of Zn because of both low n and the lowest thermal conductivity (κ) (1.085 W m−1·K−1). The total κ decreased as increasing zinc concentration in the thin films. It was confirmed that the decrease of total κ was dominated by electron κ rather than lattice κ.