The regulation of Taicang-Nantong deep-water fairway in Yangtze River is the first project of a 12.5 m deep-water fairway built in Jiangsu province. Since the river reach is located in a crossing of tidal estuary of the Yangtze River, it is characterized by a frequent alternative change in runoff and tidal flow, an intricate and changeable water and sediment movement and an acute erosion and deposition of islands and bars, so its fairway condition is highly unstable and it is difficult to be regulated. Through a long-term measurement and analysis, the regularities of riverbed evolution is discriminated and contributing factors to cause navigation-obstructing shoal zones are revealed, and an in-depth study are carried out from different regulation countermeasures such as dredging, the overall control of shapes of islands and bars and the control of key boundaries of islands and bars, thereby forming a regulation concept of“stabilizing main boundary of fairway and enhancing the ebb-tide dynamics of shoal zones”. At present, a regulation scheme of controlling the key boundary of islands and bars, and utilizing the function of a river dynamic extension project has been examined and approved, and will be implemented.