A time domain analysis procedure and method for seismic soil-structure interaction analysis are introduced in this work. This includes the selection of the soil model, the far field model, the structural model and the soil-structure interaction analysis method. The bounding surface plasticity model is implemented to model the near field. The boundary element method in the time domain is used as the far field model. A coupling method between the boundary elements and finite elements has been proposed, its main advantages being: equilibrium and compatibility conditions are used directly and the present boundary element and finite element packages only need a small modification before they are used in this coupled procedure. Nonlinear local site analyses have been carried out. The comparisons of the effects of strong and weak input motions, different soft clay sites and different input motions on local site amplification show the effect of soil yielding on local site response. A primary investigation of the effect of soil-structure interaction on structural response is carried out using the linear and nonlinear soil models. When the linear elastic model is used to represent the soil behaviour, the effects of different sites, frames and input motions from the basement rock on the soil-structure interaction are investigated. The results show that the natural vibration periods of the site and structure can represent the effect of the site and structure on the soil-structure interaction and the predominant period of the input motion can represent the effect of the input motion on soil-structure interaction. Acceleration response at the foundation, displacement at the top floor, inter-storey shear force and the rocking of the foundation are used to show the effect of the natural periods on the soil-structure interaction. When the nonlinear soil model is used to represent the soil behaviour, a comparison of the results of the linear and nonlinear analyses shows that the soil yielding has a great influence on vibration frequency and vibration amplitude of both the acceleration and the displacement at the foundation and at the top floor of the structures. The permanent settlement of the foundation shows its accumulative characteristics.