Flywheel batteries have been widely used in the aerospace and transportation fields due to their advantages of high power, fast response, and high efficiency. Among them, the magnetic levitation bearing is the key to realize the high-speed and high-efficiency operation of flywheel batteries. In this paper, the research object is the flywheel battery for automotive applications. First, the third-order critical mode characteristics of the flywheel battery are analyzed and the topology scheme of the flywheel battery support structure is designed. Then, the radial magnetic levitation bearing rotor and stator are designed, and the axial magnetic levitation bearing stator and thrust disk are designed. The closed-loop differential control strategy of the magnetic bearing is designed. The system control transfer function is derived. Finally, the strength of magnetic induction in the axial magnetic bearing is verified. The influence of the excitation mode of the radial magnetic bearing on the magnetic circuit distribution and magnetic pole coupling is analyzed, and the NNSS type topology scheme is determined. The dynamic response characteristics of the bearing system are analyzed, and the designed magnetic levitation bearing can levitate the flywheel rotor according to the operational requirements when influenced by external steps and sinusoidal excitation.