The magnetic levitation reaction flywheel (MLRW) is a novel actuator of spacecraft attitude control because of its significant advantages, including lack of friction and active suppression of vibration. However, in a vacuum environment, the poor heat dissipation conditions make it more sensitive to various losses and rises in temperature. Therefore, increasing temperature is the key issue for components used in space. In this study, the losses of the three kinds of heat-generating areas in the MLRW, namely, the passive magnetic bearing (PMB), the active magnetic bearing (AMB) and brushless DC motor (BLDCM), were analyzed and calculated. Based on the electromagnetic field theory, the loss model of PMB was proposed. Based on the finite element method (FEM) and Bertotti model, the loss power of the AMB and the BLDCM was obtained. The calculated loss values were brought into the FEM to calculate the temperature field distribution of the MLRW system. Then, the key factors affecting the heat dissipation of the flywheel were obtained by combining thermal network analysis with the temperature field distribution. Finally, a prototype was fabricated. The maximum estimated and experimental temperatures were 34.8 °C and 36.8 °C, respectively, both at the BLDCM stator. The maximum error was 5.4%, which validates the calculated model.