Recently, the development of SiC and GaN high-performance semiconductor devices has led to higher efficiency in power conversion equipment. In order to perform thermal design of power conversion equipment and evaluation of the equipment, it is necessary to measure the power loss of the equipment with high accuracy. In a previous study, a system to measure the power loss from the amount of heat emitted from power conversion devices using a Peltier device was proposed. In this study, aiming to improve the measurement accuracy, the temperature dependence of the thermal conductivity of a Peltier device, which was treated as a constant value in the previous study, was considered. The control system considering the temperature dependence of the thermal conductivity was designed based on operator theory, which is a nonlinear control theory. The simulation and experimental results show that the measurement accuracy was improved when the power loss was 10 W and 15 W compared to the case without considering the temperature dependence. In addition, the measurement time was reduced by about 100 s by considering the temperature dependence. The effectiveness of the proposed system was shown when the power loss was 10 W and 15 W.