In order to reveal the deformation and mechanical properties of highway tunnels crossing active faults in the western region of China, the misalignment response of the tunnel structure under the left-turn slip fault were analyzed by numerical simulation, the zoning of the tunnel affected by the fault slip was established, and the articulated design of the tunnel section lining was proposed as a measure to resist the fault slip. By comparing the stress and displacement response of the tunnel structure when different lengths of segmental lining were set up in the affected area, the optimal lining segmental arrangement was derived. The results show as follows. When the fault slips 2.5 m, the tunnel structure is affected by the fault within 2.7 d (d is the diameter of the tunnel) near the interface between the fault and the active disk, defining 1 d ~ 2.7 d as the secondary impact area, and 1 d as the main impact area. Through comparative analysis, it is found that the 3 m section has the best control effect on the horizontal displacement and maximum shear stress of the lining structure, and the maximum reduction rate of the peak reaches 3.38% and the maximum shear stress along the longitudinal direction of the tunnel structure is concentrated in the misalignment zone, and the changes in this range are more dramatic than those outside this range, so the misalignment zone is the key target of anti-fault misalignment prevention. The results of the study can provide a reference for the design of the tunnel against fault.