The invention provides a micro-grid voltage perturbation control system. The micro-grid voltage perturbation control system comprises an energy storage unit, a converter unit, a coordinate transformation and active power calculation unit, a power controller, a voltage controller, a self-adaptive amplitude limiter, a current controller and a PWM generator. The active current reference value output by the power controller and the reactive current reference value output by the voltage controller are subjected to an amplitude limiting process carried out by the self-adaptive amplitude limiter, and the self-adaptive amplitude limiter outputs the active reference current and the reactive reference current. Voltage control signals are subjected to a pulse width modulation (PWM) process by the PWN generator to generate PWM waveforms, and the PWM waveforms are input to the converter unit. By employing the control system and method, technical problems in the prior that the voltage in the micro-grid fluctuates frequently and the reactive power is difficult to distribute optimally are solved, so that voltage fluctuation in the micro-grid is effectively inhibited, and the voltage operation stability is guaranteed.