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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 applies different reference powers to each of the two loads simultaneously. Through modulating the phase of carrier waves, the power applied to the loads is independently controlled. The temperature of the two-phase load is controlled based on a thermal model of each load. The proposed temperature control method calculates the output power required to follow the reference temperature. Then the calculated power is 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 a temperature sensor is low. The validity of the proposed method based on independent control is verified by simulation and experimental results.