In order to keep constant DC-link voltage of a flywheel energy storage system (FESS) discharge in a wide rotational speed range, the control structure of the FESS is comprised of an inner current loop and an outer DC-link voltage loop. Since the dynamic equation of the DC-link voltage in the FESS discharge is nonlinear, it is difficult for some controllers to make the DC-link voltage in discharge be constant as the rotational speed is varying in a large range. Considering the nonlinearity of the DC-link voltage in discharge and the fast discharge requirements of the FESS, an immersion and invariance manifold (I&IM) adaptive nonlinear controller for a constant DC-link voltage is proposed via methodology of immersed in the invariant manifold. The stability of the control algorithm and the influence of the parameter error on the stability are verified by the Lyapunov stability theory, and the influence of the parameters error on the steady state and transient characteristics of the closed-loop system is analyzed numerically. It is proved that the closed-loop system satisfies the global uniform asymptotic stability conditions at the equilibrium point, and the error of the model parameters does not affect the equilibrium point of the system. Finally, the effectiveness of the I&IM adaptive nonlinear controller were studied by simulation and experiment. The results show that the DC-link voltage in discharge remains stable when switching the system load in cases of different rotational speeds and loads. INDEX TERMS Flywheel energy storage system (FESS), bus voltage, immersion and invariance manifold (I&IM), Lyapunov stability, adaptive nonlinear controller.