Asymmetrical up-and-down structure of basement rocks beneath the western part of Kanto Plain has been first recognized, based on a new geological interpretation of geophysical data. Many half-grabens, formed when the Japan Sea opened (ca. 16.5-15.0 million years ago), cause this complicated basement structure. Simulation analysis strongly suggests that a long-period ground motion, especially of around 4s components, would be amplified by such deep geological structure. As this period (4s) matches the own period of high-rise buildings of about 200m tall, it is necessary to recognize subsurface geologic structure in the Tokyo metropolitan areas.