The invention discloses a control system and a control method of a flow battery system. The control system comprises a battery management system which is connected with a plurality of galvanic pile groups. The battery management system comprises a detection unit, a judging unit, a calculation unit and a control unit, wherein the detection unit is used for detecting actual output power of the flow battery system; the judging unit is used for judging whether the actual output power of the flow battery system is lower than a preset power or not; the calculation unit is used for calculating the quantity of the needed galvanic pile groups according to the actual output power of the flow battery system and rated output power of each galvanic pile group when the actual output power of the flow battery system is lower than the preset power; the control unit is used for controlling the work state of each galvanic pile group so as to enable the quantity of the galvanic pile groups under the running state to be equal to that of the needed galvanic pile groups. By adopting the control system and the control method, not only can the efficiency of the flow batter system be improved, but also the service life and efficiency of the galvanic pile groups can always stay at an optimal state, the electrolyte is unnecessary to flow into each galvanic pile, and the self-discharging phenomenon caused by the playing and migration of electrolyte when passing an ion exchanging membrane can be reduced.