Abstract: The seismic response analysis of marine engineering structures is important to ensure the seismic safety of these structures. Marine engineering structures are always built in a complex environment where there are both water and soil. So both fluid-structure interaction and soil-structure interaction need to be considered in seismic response analysis of marine engineering structures. This paper is based on the unified calculation framework for wave motion in water-saturated seabed-bedrock system, and uses the Davidenkov model and modified Masing rule to describe the nonlinear characteristics of saturated seabed. The dynamic responses of marine sites and marine engineering structures when the pulse SV wave incident vertically are analyzed. First, the nonlinear responses of marine sites under the input of linear free field and nonlinear free field are analyzed comparatively. The results show that the nonlinear response of the marine site under the input of the linear free field is unreasonable. So it means the consistent constitutive model should be used for the free field analysis and finite element analysis of marine site. Then, the characteristics of responses of the marine site and water-saturated seabed-bedrock system when the seabed is linear or nonlinear are analyzed comparatively. Compared with the case that the seabed is linear, the influence of nonlinearity on response of seabed is mainly controlled by the following two factors: on the one hand, the modulus of saturated seabed decreases because of nonlinearity, so the wave impedance ratio between saturated seabed and bedrock decreases, and then, the reflection coefficient and transmission coefficient from bedrock to saturated seabed increase, resulting in the increase of response; on the other hand, the nonlinearity of saturated seabed causes the increase of damping, resulting in the decrease of response. For the example in this paper, the effect of damping dominate the result when seabed is nonlinear.