Traditional flood control systems always have a conflict with natural ones, i.e., rivers in cities are usually straight and smooth, whereas natural ones are according to ecological mechanisms. Social and economic developments in the modern world require a new system combining ecological needs and traditional flood control system. Ecological flood control systems were put forward and defined as flood control systems with full consideration of ecological demands for sustainable development. In such systems, four aspects are promoted: connectivity of water system, landscapes of river and lakes, mobility of water bodies, and safety of flood control. In Phoenix Island, Huzhou, needs for ecological flood controls were analyzed from the four aspects above. The Water system layout was adjusted with the water surface ratio, which is the ratio of water surface area (including rivers, lakes, and other water bodies) to the total drainage area, and connectivity as controlling indicators. The designed water levels provided references for landscape plant selection. Mobility of the adjusted water system was analyzed, including flow direction and residence time. On the bases mentioned above, ecological flood control projects were planned with comprehensive consideration of the ecological requirements. The case study indicates that ecological needs can be integrated with flood control to develop ecological flood control systems that do not only prevent floods but also retain the ecological functions of water bodies.