The invention discloses an undisturbed switching control method of a magnetic suspension energy storage flywheel charging and discharging control system, which is used for energy storage flywheel charging and discharging switching control, guarantees that the voltage is stable and free of pulsation in the charging and discharging process, and achieves the switching time of 0. According to the method, voltage outer loop and current inner loop control is adopted in the charging process, the discharging process and the charging and discharging switching process, when the direct-current bus voltage Udc is greater than a voltage stabilization value Vref set by a flywheel, the output of a voltage outer loop proportional integral link is positive, a three-phase bridge works in an inversion state,the flywheel accelerates charging, and conversion from electric energy to kinetic energy is achieved; when the direct-current bus voltage Udc is less than the flywheel voltage stabilization value Vref due to mains supply power failure or power insufficiency, the output of the voltage outer loop proportional integral link is negative, the three-phase bridge works in a controllable rectification state, and conversion from mechanical energy to electric energy is achieved. Because the whole process of the voltage outer loop is controlled in real time, the method essentially solves the problem ofcurrent and voltage fluctuation during charging and discharging switching of the energy storage flywheel, and improves the dynamic response speed and power supply quality of the flywheel battery.