During the 1995 Hyogoken-Nanbu earthquake, underground RC structures experienced significant damages which had never been experienced before. To evaluate these damages, a linear earthquake response analysis in frequency domain has often been used. For more accurate evaluation of the damages, however, a nonlinear earthquake response analysis in time domain must be employed by incorporating the continuous change of stiffness and hysteresis damping of soil-structure interaction systems. In this study, a hybrid method which combines a soil-structure interaction program, KIESSI-2D with a general purpose FEM package, ANSYS, is used to perform nonlinear earthquake response analysis of soil-structure interaction in time domain. As a verification of the hybrid method and analysis model, nonlinear earthquake response analyses are performed on the Kamisawa subway station which was damaged severely during the Kobe earthquake and analytical results are compared with the real damages. In order to consider the nonlinearity of soil, SHAKE program is used, whereas Hognestad model is used to consider the nonlinearity of concrete. It is shown that the analytical prediction agrees fairly well with the actual damages which were caused by the shear failure of the center column of the station.