The water hammer effect in the pipeline of long span cable-stayed pipeline bridges often has an great adverse influence on the bridge structure safety. The finite element model of a cable-stayed pipeline bridge was established to comparatively analyze the dynamic characteristics of water-pipe-bridge structure, and the pipe-bridge resonance check was carried out. The basic equation of water hammer is solved by the characteristic line method, then the water hammer pressure generated by different valve closing time in the process of water conveyance condition conversion was calculated to analyze the dynamic response of the main components of the pipeline bridge under the impact of water hammer and the effects of different loading modes of water hammer load and different valve closing time on the response of the components of the pipeline bridge. The results show that the natural vibration frequencies of cable-stayed bridge and water conveyance pipeline are quite different from each other whether there is no water or full of water in the pipeline, so the pipe-bridge resonance will not occur. The non-uniform loading mode significantly increases the dynamic response of each component of the pipeline bridge, and both the increment of displacement and stress are more than 50%, but they will not cause the instability or failure of the components. With the increase of valve closing time, the impact of water hammer is weakened, and the dynamic response of the main components decreases, of which the response of the K-type support rod, beam and ventral rod in the steel truss beam assembly decreases significantly, while that of the bridge tower only decreases slightly.