An individual fault dislocation or seismic effect is often considered to investigate the deformation and failure of a fault-crossing tunnel, while emerged in high-intensity seismic zones, it will be likely to subject to a superimposed effect from fault dislocation and strong seismic excitation. In this study, a three-dimension numerical model to simulate fault dislocation and subsequently dynamic response characteristics of fault-crossing tunnel was established, in which fault dislocation and earthquake levels at the site of interest. The nonlinear damage feature of tunnel was considered to furtherly reveal damage states of tunnel under the superimposed effect. And then, a quasi-static large-scale model test was performed to verify the correctness of pre-order fault dislocation calculation results. The results showed that only when the tunnel was subjected to fault dislocation, a prominent relative deformation of tunnel exists in the fault fracture zone and tension and compression zone were noticeably identified at the convex and concave zones respectively. After superimposing the seismic loading, acceleration and equivalence plastic strain amplification of tunnel near the fault fracture zone is great of significance and the damage of the tunnel under the fault dislocation was concentrated at the fault core. More importantly, the fault-crossing tunnel is more of sensitivity to the initial fault dislocation from the obvious rising on the tension damage index, and when PGA is greater than 0.2 g, the tunnel emerged in the host rock mass should also be paid more attentions, not only the tunnel in the potential fault-affected zone.