The invention discloses a water level control system of an INBA system. The water level control system comprises a water storage tank, wherein a fixed frame which is hollow is arranged in the water storage tank; a buoy is arranged in the fixed frame; an upper limit sensor is mounted on the upper part of the fixed frame; a lower limit sensor is mounted on the middle lower part of the fixed frame; the upper limit sensor and the lower limit sensor are connected with a signal detecting system through a through hole in the upper portion of the water storage tank; the signal detecting system is connected with a control system; and one side, away from the fixed frame, of the water storage tank is equipped with a water draining system, a water supplementing system, a water using hole and a water return hole. The invention further discloses a water level control method of the INBA system. According to the water level control system disclosed by the invention, the buoy can provide a most accurate signal for the liquid level; and a plurality of groups of partitions improve liquid level signal detection accuracy. The water level control system can perform reasonable water supplementing and draining according to liquid level of the water storage tank, guarantees use stability of the INBA system, avoids waste of water resources, and reduces production cost.