In order to estimate the viscous effects of clay over a wide range of strain levels, we confirmed the performance of a viscoelastic-viscoplastic constitutive model by simulating cyclic undrained triaxial tests to determine the cyclic strength and deformation characteristics of natural marine clay. The viscoelastic-viscoplastic constitutive model was then incorporated into an effective stress-based seismic response analysis to estimate the effects of an intermediate clay layer on the behavior of sand layers. Seismic response was simulated by the cyclic viscoelastic-viscoplastic constitutive model created with data recorded at Rokko Island, Kobe, Japan. The results show that a cyclic viscoelastic-viscoplastic constitutive model can provide a good description of dynamic behavior including viscoelastic effects, within a small strain range.