The aim, of this study is to examine the refuge system under storm surge flooding in an urban bay area. First, through the overland flood flow computations under the various breach point conditions, a two-dimensional horizontal distribution of the maximum overland flood flow depth (a flood hazard map due to storm surge) is obtained. Next, a numerical model is developed which can simulate the behavior of evacuee in flooding caused by storm surge, and the characteristics of evacuation system is examined. By this study, the importance of evacuation order and the danger of refuge after inundation are presented. These results show that evacuee should take refuge before inundation.