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Investigating dynamic responses and damage modes of tunnels constructed in different geological conditions is of great significance to understand the damage mechanism and put forward mitigation measures. In this paper, large-scale shaking table tests with the similarity ratio of 1:12 were used to study the seismic response (acceleration and spectrum characteristics, hoop strain, dynamic earth pressure, and longitudinal strain) of shallow buried elliptical tunnels motivated by different dynamic loads. Three different conditions of tunnel section were discussed: with shock-absorbing layer (SAL), with fault, and without SAL and fault. Then the slipping and expanding displacement, dynamic stress concentration, and damage modes of the tunnel across the fault fracture zone were studied based on numerical simulations. The research results illustrate that the presence of SAL has slight influences on amplifying the peak acceleration of the excitation motions and controlling the longitudinal strain, but it could effectively mitigate the motion energy and dynamic earth pressure around tunnels; it also demonstrates that the SAL can be utilized as a damping layer to weaken the seismic waves. Additionally, tunnels in the fault fracture zone perform remarkable dynamic response than those in the normal surrounding rock; the largest slipping and expanding displacement of fault often occur at the moment when the acceleration of the excitation motion reaches its high value. [ABSTRACT FROM AUTHOR]