Vernier-gimballing magnetically suspended flywheel is often used for attitude control and interference suppression of spacecrafts. Due to the special structure of the conical magnetic bearing, the radial component generated by the axial magnetic force and the change of the magnetic air gap will cause the nonlinearity of stiffness and disturbance. That will lead to not only poor stability of the suspension control system but also unsatisfactory tracking accuracy of the rotor position. To solve the nonlinear problem of the system, this article proposes a proportional–integral–derivative neural network control scheme. First, the rotor model considering the nonlinear variation of disturbance and stiffness parameters is established. Then, the weight of neural network is adjusted by the gradient descent method online to ensure the accurate output of magnetic force. Finally, the convergence analysis is carried out based on the Lyapunov stability theory. Compared with the general proportional–integral–derivative control and the radial basis function neural network control, the simulation results demonstrate that the proposed method has the highest tracking accuracy and excellent performance in improving stability. The experimental results prove the correctness of the theoretical analysis and the validity of the proposed method.