When a structure is constructed at the site composed of soil, the behavior of a structure is much affected by the characteristics of soil. Therefore, the effect of soil-structure interaction is an important consideration in the design of a structure at the site composed of soil. Precise analysis of soil-structure interaction requires a proper description of soil profile. However, most of approaches are nearly unpractical for soil exhibiting material discontinuity and complex geometry since those cannot consider precisely complicated soil profiles. To overcome these difficulties, an improved integration method is adopted and enables to integrate easily over an element with material discontinuity. As a result the mesh can be generated rapidly and highly structured, leading to regular and precise stiffness matrix. The influence of soil profile on the response is examined by the presented method. It is seen that the presented method can be easily used on soil-structure interaction problems with complicated soil profile and produce reliable results regardless of material discontinuities.