To meet the thermal design requirements of an attitude control flywheel system for small satellites, the thermal performance of the flywheel system was analyzed and an experimental verification was carried out. According to the flywheel operating conditions, the electronically controlled loss and the mechanical loss of the flywheel system were calculated in theory to determine the distribution of the main heat source of the system. Then, an equivalent thermal network model was established based on the whole mechanical topology structure. The Finite Element Method (FEM) was applied to analysis of the thermal performance of the main components and the whole system under the swinging condition, respectively. Finally, a prototype was developed and the thermal vacuum test was carried out to validate the analysis results. The results show that the final equilibrium temperature of the monitoring point is about 57.8 ℃ under the swinging operating condition for 8 hours with the ambient temperature 45.0 ℃. The error is 8.6% relative to the FEM result of 53.2 ℃, which indicates that the temperature values obtained in the analysis and the experiment are coincident with well and the thermal design meets the thermal requirements of the satellite systems. This analysis provides an important reference for the thermal design of attitude control flywheel systems.