Dynamic response records of tunnel in inhomogeneous ground condition, particularly in an extreme case of soil-rock strata, are limited due to the challenges of recording the seismic soil-structure interaction (SSI). This study aims to build a 3D numerical model based on a shaking table test conducted at Tongji University. In the numerical process, the nonlinear dynamic behavior of the model soil is captured by a kinematic hardening constitutive model, while the model rock and tunnel are assumed to remain in the elastic regime. Numerical results show good consistency with the experimental data, indicating that the validated FE model can be used for further investigation of the influences of relevant parameters on dynamic responses of tunnel in soil-rock strata. A key conclusion in this study is that the abrupt change of ground stiffness leads to concentration of joint deformation near the interface.