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 This paper proposes a model-based temperature control method for a three-leg two-phase inverter with independent control for each phase load. In the proposed method, a three-leg two-phase inverter simultaneously applies different reference powers to each of the two loads. Through modulating the phase of carrier waves, the power applied to the loads is controlled independently. The temperature of the two-phase load is controlled based on the thermal model of each load. The proposed temperature control method calculates the output power required to follow the reference temperature. The calculated power is then independently applied to each load. In addition, this paper proposes a compensation method to improve the performance of the proposed temperature control method when the resolution of the temperature sensor is low. The validity of the proposed method based on independent control is verified by simulation and experimental results.