A battery cell balancing control system and a battery management method thereof are disclosed. The battery cell balancing control system is used for managing a battery apparatus, wherein the battery apparatus has a plurality of battery cells. The battery cell balancing control system comprises a detection module, a battery management module, and an adjusting module. The detection module is used for executing a battery checking procedure on the plurality of battery cells to generate a detection result. The battery management module is used for determining whether the plurality of battery cells has a controlled cell according to the detection result. If the controlled cell has not been found among the plurality of battery cells, the battery management module controls the adjusting module to execute a battery cell balancing procedure until the controlled cell is found.