In2O3/ITO thin film thermocouples (TFTCs) with alumina protecting layer were fabricated on alumina substrates. The effects of protecting layer on their performance at higher temperature and long term service were investigated accordingly. In2O3 and ITO thin films were prepared by radio frequency magnetron sputtering methods, while the alumina protecting layer was prepared by traditional spin-coating methods. Microstructural and thermoelectric properties of the In2O3/ITO TFTCs with and without alumina (Al2O3) protecting layer were investigated as a function of sintering time from 2 to 10 h at 1250 °C. The results show that, the existence of alumina protecting layer can effectively increase the performance capabilities of thermocouples at high temperatures by inhibiting the volatilization of the thin film. In2O3/ITO TFTCs with protecting layer can work normally over 10 h at 1250 °C while Seebeck coefficient is 131.7 µV/°C. The drift rate can reach 3.05 °C/h, which is much better than those without protecting layer.