The Daxing project is connected with the southern main channel and Langzhuo main channel respectively, which not only realizes the water interconnection between Beijing and Hebei, but also provides a two-water-sources channel for the waterworks of the new airport in Beijing. In the actual operation, according to the different demands of southern main channel, Langzhuo main channel and the waterworks of the new airport, unsteady flow will be caused because of the switch between the two water sources and opening and closing the valves. Too high pressure can cause the pipe to break, and too low pressure can cause it to collapse and damage valves and fixtures. Therefore, in this study, an unsteady flow numerical simulation model is established using characteristic method. Then the maximum and minimum water hammer pressure and their locations are calculated. On the basis, the water hammer protection measures are proposed, and the effect of water hammer protection measures are analyzed. Finally, the results show that the proper arrangement of the air valve and the proper closing sequence and closing law of valves can effectively protect the system from water hammer and ensure the safe operation of the project.