The invention provides a wind power generation-based electric energy quality compensation controlling apparatus and a method thereof. The apparatus consists of a wind power-electricity energy conversion module, a central control module, a direct-current processing module, an alternating-current voltage transformer module, an H bridge inverter module and a bypass thyristor module. The central control module measures a current value and a voltage value of the direct current by the direct-current processing module, calculates a real-time output power of the direct-current processing module and carries out maximum power tracking on the direct-current processing module; and the alternating-current voltage transformer module measures a voltage value of an alternating-current power grid. When the central control module detects that the voltage value of the alternating-current power grid is lower than a preset range of a rated voltage value preset by the alternating-current power grid, the bypass thyristor module is controlled to be turned off; and the H bridge inverter module is controlled to compensate the alternating-current power grid for a difference voltage value between the rated voltage value preset by the alternating-current power grid and the alternating-current power grid voltage value. The provided wind power generation-based electric energy quality compensation controlling apparatus does not employ a series transformer, so that the size of the apparatus is small and the cost is low.