Fault-crossing tunnel structures were severely damaged by fault movement during Wenchuan Earthquake. This phenomenon demonstrates that traditional aseismic technologies cannot guarantee the security of tunnel and underground structures. Therefore, new types of deformable aseismic and damping measures have to be developed for tunnel and underground structures. Shaking table tests are conducted to investigate seismic response characteristics and post-seismic destructive patterns of tunnel structures with these measures. The results show that the absorbing joint can reduce the internal forces and the strains of fault-crossing tunnel structures. The casing-shape damping measure can effectively protect both the inner casing and most parts of outer casing structures except for the arch springing and tunnel invert of the outer casing. The casing-shape damping measure performs better than the absorbing joint, since the former can improve the waterproofing quality and recoverability of tunnel structures besides the aseismic capacity. It is necessary to enhance the intensity of secondary lining concrete when using deformable aseismic and damping measures. No matter what kind of aseismic measures are employed, the arch springing and tunnel invert parts are needed to be reinforced. The above research results can provide references for seismic fortification of tunnel and underground structures across geological hazards zones.