The invention provides a water-secluding pipe filling valve control system for a marine drilling platform. The water-secluding pipe filling valve control system comprises a balance valve, a control valve, a lock valve, a change-over valve, an energy accumulator and a drive oil cylinder, wherein the control valve separately communicates with the balance valve and the lock valve through oil tubes; the change-over valve separately communicates with the lock valve, the energy accumulator and the drive oil cylinder; and the control valve is additionally equipped with a remote control interface, and the control valve communicates with an external hydraulic control source through the remote control interface. A using method for the water-secluding pipe filling valve control system comprises five steps of system initialization, system pressure drop, filling valve opening, opening keeping and filling valve closing. The system provided by the invention is simple in structure, is high in fault resistance, is various and flexible in control way, and is good in operation stability and interference resistance, so that automation degree, reliability and stability of filling valve operation are improved, and the defects such as low filling valve control speed and low implementation precision as a result of balance valve pressure difference in a conventional control system are effectively solved, and therefore, control precision of the water-secluding pipe filling valve control system is greatly improved.