This paper studied the nonlinear dynamics of electromechanical coupling between the flywheel and the generator in the flywheel energy storage system (FESS) based on active magnetic bearings (AMBs). By deducing the functions of the kinetic energy, the potential energy, the magnetic field energy in the air gap of the generator and the energy dissipation of the whole system with rotor eccentricity, the dynamical equations of the coupled system between the flywheel system with AMBs and the twophasefourpole permanent magnet generator were established by using the LagrangeMaxwell equation. Then, the numerical method was adopted to analyze the nonlinear dynamical characters of the 0.6MW FESS based on AMBs, and the analytical results of the example show that the stable rotatingsynchronous harmonic solution and tripleharmonic solution exist in the nonlinear equations of the coupled system, and the amplitude of the synchronous vibration is higher than that of tripleharmonic vibration. Furthermore, when the FESS based on AMBs is stable, the nonlinear vibration can be weakened by increasing rotational speed of flywheel, the damping of AMBs or by decreasing the stiffness of AMBs, the magnetic field energy which includes the armature reaction energy and the permanent magnet excitation energy. As for decreasing the damping of AMBs or by increasing the stiffness, magnetic field energy, the flywheel may get unstable.