This study addresses the water hammer protection challenges in the JH gravity-fed bifurcated pipeline network system in Xinjiang, China. A hydraulic transient numerical model is developed using the one-dimensional method of characteristics and implemented in Bentley HAMMER software to systematically analyze the transient response characteristics under different valve closure schemes, with a focus on revealing pressure fluctuation patterns in branch and main pipelines under various shutdown modes. Key findings include the following: Single-valve linear slow closure reduces the maximum water hammer pressure by 54.7%, while the two-stage closure strategy suppresses pressure extremes below safety thresholds with 73.1% higher efficiency than linear closure. For multi-valve conditions, although two-stage closure eliminates negative pressure risks, most of nodes exhibit transient overpressure exceeding 1.5 times the working pressure. By integrating overpressure relief valves into a composite protection system, the maximum transient pressure is strictly controlled within 1.5× rated pressure, and the minimum pressure remains above −2 mH₂O, successfully resolving protection challenges in this complex network. These results provide technical guidelines for the safe operation of gravity-fed pipeline systems in high-elevation-difference regions.