In designing crown heights of coastal protection facilities, deciding sea level departure from normal is very important. Formally, the way of deciding sea leve departure from normal along the coasts of Tokyo Bay hasn't been consistent. So we have developed a new model of storm surge simulation and calculated sea level departures from normal along all the coasts. We inspected the crown heights of coastal protection facilities by using the simulated results and found some areaswhere storm surges may cause overflow. We propose that the simulated results areused in designing the crown heights of coastal protection facilities hereafter.