Even if numerous studies were dedicated to propose soil-structure interaction analysis methods, most of these methods introduce several assumptions to circumvent the difficulties encountered in modeling and reduce computational efforts. The complex spatial configuration of the soil-foundation interface or the distribution of the soil medium are often simplified using flat-layered soil profiles and, the nonlinearity of the soil medium is generally dealt through an equivalent linear model. However, real soil profiles are featured by complex shapes, inclusion of discontinuities and nonlinear characteristics of soil. Accordingly, this paper presents a soil-structure interaction analysis method considering the characteristics of the structure, soil-structure interface and complex nonlinear distribution of the soil that could not be accurately modeled in previous methods. The proposed method adopts unaligned mesh generation and nonlinear modeling approach to model complex soil profiles. The validity and applicability of the nonlinear soil-structure interaction analysis method are verified through a numerical example.