Some cut and cover tunnels were damaged by the Hyogoken-Nambu Earthquake in 1995. In most cases, except for important facilities and those constructed in soft subsoil, a seismic resistant design had not been considered. And its design method was not for such large earthquakes. From this viewpoint, a new seismic design method of cut and cover tunnels for larger earthquakes is desired. To investigate the behavior of underground structures at the time of earthquake, damage of three underground structures is first investigated and analytical simulations are carried out. Several model shaking table tests of cut and cover tunnel are then performed and the results are numerically analyzed. Finally, a new seismic design method of cut and cover tunnel is presented based on these test and analysis results.