In order to effectively protect long-distance, multi-undulation, and high-fall gravity-flow water pipelines, a hydraulic transition process calculation model was established for an actual project based on the wave characteristic method. The value closure laws without protection measures were analyzed, the protection effects of traditional common air valve and three-action air valve were compared, and the impact of the combination of the three-action air valve and two-stage valve closure on water hammer was investigated. The results show that without protective measures, the minimum pressure along the entire pipeline seriously exceeds the standard. After adopting the combination of the three-action air valve and two-stage valve closure, the minimum pressure head of the water pipeline can be maintained above -2 m. For long-distance, multi-undulation, and high-fall gravity-flow water pipelines, priority should be given to reducing the negative pressure in the pipeline. The use of the combination of the three-action air valve and two-stage valve closure can have a good control effect on the negative pressure in the water pipeline and in front of the valve.