The flexible bearing is the key component of the harmonic reducer. In the work, it keeps elastic deformation with the rotation of the wave generator, and large amount of heat is generated due to friction and viscous shear of lubricant. If the heat can’t be distributed effectively, the high temperature will cause the thermal deformation and the premature fatigue failure of bearing, and ultimately reduce the efficiency and service life of the reducer. Therefore, it is very important to study the thermal stress distribution of inner and outer ring for the design and life calculation of flexible bearings. The multi-body contact model and thermal model of the flexible bearing were established by ANSYS Workbench. According to the analysis results of static stress, the friction torque of the flexible bearing is calculated and the calculation model of heat capacity for flexible bearings is established. Finally, the steady state thermal analysis of the bearing is carried out, and the temperature distribution of the inner and outer ring and the ball is obtained. The research results provide theoretical reference and guidance for the design of flexible bearings.