This paper describes the effects of subsurface structure on ground motions and nonlinear responses of super high-rise RC buildings to pulse-like ground motions using subsurface structure models from the seismic bedrock to the ground surface in the Tokyo Metropolitan area. Amplification of pulse-like ground motions and relatively large story drift of upper buildings are remarkably seen in the area between Sumida and Edo Rivers. The shallow part of subsurface structure is dominant for the ground motion amplification and consequent structural responses rather than deep part mainly due to nonlinear soil responses in the low Vs sediments. © 2022 Architectural Institute of Japan. All rights reserved.