The invention provides an active power and reactive power coordination control method of a wind turbine generator system and a system thereof. The method comprises the steps of judging whether the impedance angle of an outgoing line of a wind turbine generator system exceeds an impedance angle preset range or not; if the impedance angle of the outgoing line of the wind turbine generator system does not exceed the impedance angle preset range, setting the wind turbine generator system to run at a unity power factor; otherwise, monitoring the active power of the wind turbine generator system andthe voltage of a grid-connected point, and calculating the required reactive power of the wind turbine generator system when the voltage of the grid-connected point exceeds a preset range; if the required reactive power of the wind turbine generator system does not exceed the reactive power output limit of the wind turbine generator system, outputting the required reactive power by the wind turbine generator system; otherwise, outputting a reactive power maximum value when the reactive power of the wind turbine generator system is greater than 0; calculating the active power of the wind turbine generator system according to the preset voltage of the grid-connected point and the voltage of the grid-connected point after the fully exerting of the reactive power regulating capability of thewind turbine generator system and when the reactive power of the wind turbine generator system is smaller than 0. According to the technical scheme of the invention, the operating efficiency and the grid-connection adaptability of the wind turbine generator system, and the supporting capability of the power grid are improved.