Due to Shanghai’s unique location, it is sensitive to sea level rise and land subsidence, which are directly related to urban flood protection. Flooding of Shanghai can be caused due to the following three factors: storm surge by typhoon, high tidal levels and sustained higher water levels in the Yangtze River and the Huangpu River as a result of the higher tide in the mouth of the river during the rainy season. Typhoons moving towards Shanghai not only bring high storm surges but also heavy rainfalls and strong winds to the area. In response to the potential floods caused by typhoons to Shanghai city, China, several proposals emerged to protect the region in the first design level. By using Multi Criteria Analysis, one of them is selected as the protection system. A challenge for this 15 km long barrier system is to cross Yangtze Estuary, including two islands and three channels at the Yangtze River mouth. This thesis, based on a system engineering approach, presents the design process and a feasible design for the storm surge barrier system at this specific site.