In the past, a number of approaches, such as analytical, numerical or experimental methods, have been developed to deal with the soil-structure interaction effects. However, for many problems with complex geometry and material discontinuity most of approaches are nearly unpractical since it is difficult to model structures and complicated soil profiles precisely. This paper presents a soil-structure interaction analysis approach, which carl consider precisely characteristics of structures and complicated soil profiles. The presented approach overcomes the difficulties by adopting an unaligned mesh generation approach. From numerical examples, the applicability of the proposed approach is validated and dynamic responses of soil-structure systems subjected to earthquake loading are investigated considering characteristics of structures and complicated soil profiles.