To address the challenges of faulting, leakage, and other damages in longitudinal deformation joints of tunnels in strong earthquake zones, which can lead to structural failure under seismic action, this paper systematically analyzes the failure mechanisms and existing technical shortcomings of fault-resistance structures in longitudinal deformation joints based on the seismic response characteristics of tunnels in such zones. By reviewing damage cases of tunnel deformation joints in the Wenchuan and Jiuzhaigou earthquakes, three typical failure modes are identified: “tearing of rubber waterstops, crushing of filling materials between joints, and detachment of anchoring structures.” The core cause lies in the inadequate adaptation of structural design to the load characteristics of “large displacement and high stress” in strong earthquake zones. In response, a three-dimensional optimization technology system encompassing “materials-structure-construction” is proposed: At the material level, a composite waterstop material with high elasticity and aging resistance is developed; at the structural level, an innovative combined structure of “mortise-tenon type limit + multiple waterstops” is introduced; and at the construction level, a quality control process of “precise positioning-layered pouring-dynamic monitoring” is established. Numerical simulations and model tests demonstrate that the optimized structure can withstand ± 150mm longitudinal dislocation and ± 80mm transverse displacement, reducing leakage by over 90% and enhancing fault-resistance by 2.3 times compared to traditional structures, providing crucial technical support for the seismic safety of tunnel engineering in strong earthquake zones.