Abstract: Nonlinear models of the active magnetic bearing and permanent magnet synchronous motor are built respectively based on the alternative mapping method, and combined with flywheel rotor dynamics module, PID controller and other components to construct a coupled nonlinear dynamic system model of the high-speed flywheel rotor. The simulation results show that the calculation error of the permanent magnet synchronous motor cogging torque between the alternative mapping model and the finite element model result is tiny.This indicates that the alternative mapping method has good accuracy, and can correctly describe the cogging torque vibration characteristics from the fundamental frequency to multiple frequencies. The eccentric force of the permanent magnet synchronous motor rotor increases as the rotor vibration amplitude increases, and it may significantly weaken the control capability of the active magnetic bearing to the flywheel rotor. Based on the double-spring model in previous studies, a three-spring model is built by combining it with the permanent magnet synchronous motor alternative mapping model. The simulation results show that the eccentric force of the permanent magnet synchronous motor rotor changes the frequency and amplitude of the second critical speed of the flywheel rotor, and a larger eccentric force and position offsets may cause motion instability around the second critical speed.