In this study, the influence of historical changes on bathymetry to the intensity and features of the storm surge in the Tokyo Bay is evaluated using the meteorology-ocean-Tide models. In detail, storm surge of 1917 is reproduced using an artificial Taisho Typhoon of 1917 in order to quantify the influence of bathymetric changes. This paper possesses two important findings. The first is that past storm surge occurred mainly because of shallow water area spanning over the inner bay which can be characteristics of past bathymetry. The second is that the high vulnerable area affected by storm surge has been shifted from mudflat shallow area in the inner bay to the below-sea-level inland area, due to landfill and urbanization which have continued approximately 100 years after the storm. As a conclusion, the bathymetry shifting due to human activity has a great influence to changing the effects of coastal disasters even in the same location.