Abstract: Deep-buried tunnels crossing large fault zones are exposed to significant risks of high-pressure water inrush and seepage instability, and their transient seepage mechanisms and risk assessment methods require further investigation. In this study, a water diversion tunnel project is investigated through high-resolution three-dimensional transient seepage numerical simulations. The internal structure of the fault zone and seepage control measures are explicitly characterized. A parabolic variational inequality (PVI) method is employed to simulate the transient seepage response during tunnel excavation, and a quantitative seepage instability risk assessment method based on a critical hydraulic gradient threshold is proposed. The results indicate that permeability heterogeneity within the fault zone is the key factor controlling the evolution of seepage pathways and seepage instability. Ground directional grouting effectively reduces water inflow but causes hydraulic head buildup outside the grouted zone, whereas pre-drainage produces a pronounced pressure-relief effect. The combined application of grouting and drainage reduces the total water inflow by 69.7% and decreases the maximum hydraulic gradient in ungrouted zones by 74.9%, bringing it below the critical instability threshold and markedly improving seepage stability. This study provides a reference for disaster risk identification and the optimization of seepage control strategies for similar deep-buried tunnel projects.