The electromechanical coupling dynamics of the flywheel energy storage system (FESS) with a hybrid permanent magnetic-dynamic spiral groove bearing has been studied. The functions of the kinetic energy, the potential energys, the magnetic field energy in air gap of the flywheel motor and the energy dissipation of the whole system were obtained, and the differential equations set with electromagnetic parameters of FESS was established by applying the extended Lagrange-Maxwell equation. The four-order implicit Runge-Kutta formula to the equations was derived, and the nonlinear algebraic equations were solved by using the Gauss-Newton method. The analytical solution of an example shows that the upper damping coefficient, the lower damping coefficient and the residual magnetic induction of the rare earth permanent magnet play an important role in electromechanical resonance of the flywheel rotor system. There is a small change for the electromechanical coupling resonance frequency with the upper damping coefficient increasing, but the resonance amplitude decreases with the upper damping coefficient increasing. With the lower damping coefficient increasing, the resonance frequency increases, and the resonance amplitude decreases. With the residual magnetic induction of the permanent magnet increasing, the resonance frequency decreases, and the resonance amplitude increases.