Analysis of soil-structure dynamic interaction subjected to seismic wave is a key problem in earthquake engineering. In general, the soil stratum consists of two-phase saturated porous zones and single-phase viscoelastic zones due to ground water. In most cases of soil-structure dynamic interaction analysis, the soil has been assumed to be a singlephase viscoelastic medium for simplicity and little attention has been paid to the saturated porous soil case, even less to case of the viscoelastic soil layered on saturated soil. In this study, an effcient method for three-dimensional saturated soil-foundation-structure dynamic interaction analysis is proposed. The unbounded saturated soil is modelled by lumpedmass explicit finite element method and transmitting boundary condition the structure is analysed through implicit finite element method, and response of the rigid foundation is calculated through explicit time integration scheme. The different time steps can be chosen for the explicit and implicit integration scheme, which can greatly improve the effciency. In addition, based on the fact that single-phase soil is a special case of two-phase saturated soil, the dynamic analysis of single-phase soil can be unified into the analysis of saturated soil by setting the bulk modulus of pore fluid and porosity to be zero. Thus, the soil-structure interaction analysis for the viscoelastic soil layered on saturated soil case is realized, which can approximate the ground water table in practice. The effects of ground water on the response of foundation and structure are examined through numerical examples of soil-structure interaction analysis for saturated soil, single-phase viscoelastic soil and the viscoelastic soil layered on saturated soil, and the results show that the ground water influences the structure and foundation responses greatly.