The ceramic spindle rotor system is widely used in CNC machine tools. However, the dynamic characteristics are influenced by the magnetic forces and thermal deformation, which leads to the reduction of running accuracy. In this paper, the thermal deformation of the rotor system are calculated, and the magnetic field distribution is obtained based on the Maxwell theory. The thermal magnetic coupling effect is then analyzed to investigate the interaction between thermal deformation and magnetic force, and the impact of thermal magnetic coupling effect on the dynamic characteristics is obtained. Experiments are conducted to verify the simulation results, and the dynamic characteristics with and without consideration of thermal magnetic coupling effect are compared. Results show that the thermal deformation and magnetic force have nonlinear increases with speed, and the model considering the thermal magnetic coupling effect has a higher accuracy with the error decreased by 4%. The air gap is a key factor that determines the dynamic characteristics of the ceramic spindle rotor system, and a larger air gap can help lower the vibration at high speed. This study provides a theoretical basis for the structural design of ceramic spindle rotor system.