As an important part of the flywheel system, magnetic bearings (MBs) worked in a vacuum environment with poor heat dissipation and high temperature, which would seriously affect the operation and reliability of the flywheel system. The loss of hybrid magnetic bearing (HMB) for flywheel energy storage was analyzed. Based on this, the 3D thermal model of HMB was established by using ANSYS finite element software. The losses of the MBs under different operating conditions were introduced into the temperature field as heat source. The temperature distribution of the MBs under different operating conditions was obtained, which provided an important basis for the design and temperature rise control of the MBs.