The invention discloses a water hammer preventing operating valve core control system, comprising a motor, a pump, an oil/water tank, a filter, a safety valve, a check valve, a pressure reducing valve, a proportional overflow valve, a servo valve, a hydraulic cylinder, a pressure difference sensor and a pressure difference controller. An inlet of the proportional overflow valve is connected with acavity of a spring cylinder; a spring of the spring cylinder is compressed through a piston rod, and the control pressure of the proportional overflow valve is converted into the displacement controlof a throttle valve core, so as to realize the switching speed controllability of a water hammer preventing operating valve core. Two pressure measurement points of the pressure difference sensor areconnected with an inlet and an outlet of the throttle valve core, so as to give pressure difference feedback to the pressure difference controller; the opening degree of the a regulating valve core through the hydraulic cylinder controlled by the servo valve, the fore-and-aft pressure difference of the throttle valve core is controlled by a closed ring, so as to realize the speed regulation on amain liquid pathway. The control system can realize the low-speed control system switching of the throttle valve core, so as to effectively inhibit and weaken water hammer.