According to the large-scale undersea immersed tunnel of the Hong Kong-Zhuhai-Macao Bridge, and based on the actual site soil geological distribution, three-dimensional refinement FEM models were built considering the siltation above the tunnel with and without siltation. The nonlinear characteristic of flexible joints, the nonlinear contact effect between the soil and tunnel, and the nonlinear behaviour of soil material were all taken into account in the calculation model. With uniform excitation and travelling wave excitation input directly on the bedrock surface, the earthquake response analysis of soil-immersed tunnel was conducted with the dynamic explicit algorithm. Numerical results have shown that the existing siltation soil above the tunnel reduces the natural frequency of soil-immersed tunnel system and increases the seismic response of tunnel. The excitation mode and excitation direction of seismic wave also have certain influence on the relative deformation of flexible joints and the internal force response of tunnel, which can not be ignored.