In order to predict the temperature rise of the high speed motor in a Magnetically Suspended Control Moment Gyroscope(MSCMG) more accurately, it is necessary to calculate the eddy current loss of the motor winding and conduct thermal analysis of the MSCMG. In this paper, the maximum angular momentum of 200 N·m·s, rated speed of 12 000 r/min MSCMG was taken as the research object. Firstly, the principle of eddy current generation was analyzed. By combining analytical method and finite element method, the eddy current loss of high-speed motor winding was deduced and calculated. Then, a three-dimensional finite element model of the MSCMG was established, and the temperature distribution was obtained by thermal analysis on the basis of the known losses. Finally, a prototype temperature rise experiment was designed for verification. The simulation results show that the stator temperature is the highest and the stator winding temperature is 40.3 ℃. The motor stator temperature measured by the temperature rise experiment is 41.6 ℃, and the error is 3.1% compared with the theoretical value. Compared with the thermal analysis without considering eddy current loss, the accuracy is improved by 3.7%. It is more accurate to predict temperature rise by considering eddy current loss in thermal analysis. The work in this paper is of great significance to optimize the thermal design of MSCMG.