The effects of polymer substrates on the interfacial structure and the thermal stability of Ga-doped ZnO (GZO) thin films were investigated. The GZO thin films were deposited on polyethylene terephthalate (PET) and polyethylene naphthalate (PEN) substrates by rf-magnetron sputtering at room temperature, and thermal stability tests of the GZO thin films on the polymer substrates were performed at 150°C up to 8 h in air. Electrical and structural characterizations of the GZO thin films on the PET and the PEN substrates were carried out, and the origins of the stable interfacial structure and the improved thermal stability of the GZO thin film on the PEN substrate were discussed.