The phenomenon of water hammer impact caused by the opening and closing of valves in large distance water transfer system of ships is prominent, which seriously threatens the operation safety and overall stealth performance of the system. In order to effectively guide the treatment of water hammer impact in water transfer system and explore the main influencing factors of water hammer pressure rise in large-distance water transfer system, a one-dimensional system simulation model is established based on the transient flow model and the design of large-distance water transfer system on a real ship. The relationship between the influencing factors such as valve closing time, water transfer pressure, pipe diameter and water hammer pressure rise is analyzed by numerical calculation. Based on the numerical test principle of single variable, the calculation results show that the pressure rise of water hammer can be effectively reduced by extending the valve closing time, reducing the water transfer pressure and increasing the pipe diameter. The research results point out the direction for the treatment of water hammer impact in the large spacing water transfer system. In the future, combined measures such as balancing the water transfer pressure of the water tank, increasing the pipe diameter, adjusting the valve controller to appropriately extend the valve closing time can be taken to suppress the destructive positive pressure water hammer and negative pressure water hammer at the moment of valve closing in the system pipeline.