To better understand how ground motion in the Tokyo Lowland is affected by the geological conditions in the shallow subsurface, we analyzed borehole logs and conducted microtremor observations along the Ueno-Koiwa survey line, which crosses the buried valley beneath the Tokyo Lowland. Remarkable peaks in the H/V spectra at ~1 Hz were found in the area of the lower buried terrace (buried flat surface 2), whereas the peaks at ~1 Hz are small in the area of the buried valley bottom with the thickest valley-filling post-Last Glacial Maximum (LGM) deposits. The sharp peaks around buried terrace 2 are generated by the large contrast in the physical properties of the soft, muddy post-LGM deposits and the underlying gravel bed, which suggests larger ground-motion amplification during an earthquake. The variation of the ground motion characteristics along the survey line obtained by microtremor observation is consistent with the distribution of seismic intensity during the 1923 Kanto Earthquake. It is, therefore, important to consider not only the thickness and physical properties of the post-LGM deposits during seismic hazard assessment, but also the total geological composition, including the Pleistocene strata below the post-LGM deposits.