In order to study the water hammer problem of a long-distance multi-branch pressurized water conveyance system composed of gravity flow pipelines and pump pressurized pipelines during startup, a mathematical model for calculating the transient process of the water conveyance system was established based on the method of characteristics. Taking an actual project as an example, the impact of different opening time and control strategies of the regulating valve and the pump and its outlet valve on water hammer was calculated during the startup period of the water conveyance system. A water hammer protection scheme using air valves in combination with valve opening was proposed. The results show that the internal water pressure along the water conveyance system can be effectively improved by adopting the strategy that the opening of pump stations lags behind the start of regulating valves and each pump station is opened successively. The water hammer protection scheme using air valves in combination with valve opening can achieve better water hammer protection effect with a smaller size of air valves without affecting the response speed of the water conveyance system.