The invention provides an intelligent control system of a filling valve of a water separating pipe of a marine drilling platform and the filling valve. The system comprises a water separating pipe body, a water separating pipe chamber door, a driving oil cylinder, a pressure sensor, a displacement sensor, a balancing valve, a control valve, a lock valve, a control solenoid valve, a conversion valve, an energy storage device and an intelligent control system body, wherein the pressure sensor, the displacement sensor, the control valve and the control solenoid valve are additionally respectively electrically connected with the intelligent control system body; the intelligent control system body comprises a data processing circuit, a communication circuit, a driving circuit, a pressure detecting circuit and a displacement detection circuit. With the adoption of the system, the filling valve of the water separating pipe has the intelligent device detecting and intelligent operating functions; therefore, the reliability and stability in device operation are improved; in addition, the defects of slow corresponding control and small performing precision of the filling valve due to excessive pressure difference of the balancing valve in the traditional control system can be effectively solved, and the operation stability and accuracy of the filling valve of the water separating pipe can be improved.