The invention discloses a charging and discharging control system and a charging and discharging control method of a flywheel battery. The system comprises a three-phase uncontrollable rectifying circuit, an energy storage filter capacitor, an insulated gate bipolar translator (IGBT) power conversion circuit, a zero passage detection circuit, a voltage detection circuit, a current detection circuit, a direct current voltage detection and overvoltage protection circuit, a sampling and filtering overcurrent protection circuit, a displacement sampling circuit, a temperature sampling circuit, a digital signal processor controller, an energy storage inductor, a three-phase linked switch and a rotary transformer signal processing circuit, wherein the energy storage inductor is connected between the output end of each phase on the alternating current side of the IGBT power conversion circuit and the input end of a flywheel motor; the three-phase linked switch is connected in parallel with the energy storage inductor respectively; and the rotary transformer signal processing circuit is connected between the signal output end of a rotary transformer of the flywheel motor and the quadrature encoder pulse (QEP) port of the DSP controller. In the method, charging and discharging control of a flywheel battery is realized based on the system. The system has stable output direct current voltage, small high-frequency ripple, quick dynamic response, and is particularly suitable for quick charging and quick discharging working conditions; and the power factor and efficiency of the system are improved greatly.