Water hammer occurring in water pipeline not only seriously threatens the safety of water transfer project, but also restricts further development of water transfer project. However, as an efficient and energy-saving method of water delivery, it is necessary to study valve closing mode of gravity flow to solve the water hammer problem. After numerical calculating with MATLAB, and analyzing two-stage adjustment of the valve, it is concluded that the mode of first closing fast and then closing slow has better control effect on water hammer than that of first closing slow and then closing fast. The influencing factors of fast closing time and fast closing amount in two-stage valve closing mode were studied. It is found that water hammer can be effectively controlled by adopting the continuous two-stage closing mode of “4 s fast closing 65%,16 s slow closing 35%”, and the closing amount of the valve is main factor affecting the surge pressure in the pipeline. After closing process is further decomposed, increasing the number of action, adopting "1 s fast closing 35%, 3 s fast closing 30%, 12 s slow closing 25%, 4 s slow closing 10%", the maximum pressure of water hammer is suppressed, and the pressure fluctuation is also improved after the valve is closed completely. It is found that the closing mode of adding a time interval between the two stages can also exert good control effect on water hammer after compared it with the continuous two-stage closing mode. Therefore, when the equipments cannot meet multiple continuous actions, the closing mode of adding a time interval between two stages can also control the water hammer in the pipeline effectively.