A thermoelectric device called a Peltier device is widely used in many fields. For example, the device is used for a cooling system such as in systems consisting of medical reagent coolants and refrigerators. However, controlling the device is difficult because thermal characteristics of the device change depending on its temperature. Notably, the amount of heat flow generated from the device varies with the amount of current applied. Therefore, a thermal nonlinear behavior has to be considered in a thermal model. Most studies do not consider the nonlinear characteristics and treat the device as a linear system. Therefore, robustness against disturbance is not high because of modeling error. This paper presents a heat disturbance observer considering the nonlinear characteristics of a Peltier device. Variable parameters depending on the temperature and current of the device are used, and a variable heat disturbance observer is proposed. The thermal model used in the proposed observer includes a few nonlinear elements such as Joule heat and heat flow inside the device. The objective of this study is to improve the response of a Peltier device. Some experiments were conducted to verify the validity of the proposed method. Besides, the effect of modeling error on the stability of the observer is discussed.