The Deepwater Channel Phase III Regulation Project of Yangtze Estuary was completed and approved in March 2010, and deepwater channel has been extended to Dangxikou of Taicang City at the end of 2010. According to the national plan, in order to give full play to the benefits of the Yangtze river golden channel, the 12.5m deepwater channel will be extended to reach Nanjing Harbor, thus about 400km long 12.5m deepwater channel will be constructed. Therefore, deepwater channel of Nanjing downstream project is carried out by Ministry of Transportation and Communication and Jiangsu Province Government. The project is another major water transportation engineering following the Yangtze estuary deepwater channel regulation project. The project will be implemented in two phases, in which phase I is located in Taicang~Nantong reach of Yangtze River, immediately following the completed Yangtze Estuary 12.5m deepwater channel. There are two major navigation-obstructing channels in this reach —— Tongzhou Shoal channel and Baimao Shoal channel. Based on preliminary works of riverbed evolution analysis, mathematical model calculation and other researches, depended on existing large-scale and wide-range Yangtze River estuary model, fixed and movable bed physical model tests were used to study the comparable feasibility scheme and optimization scheme. Through analysis, four fixed bed model and three movable bed model representative hydrodynamic conditions were considered, channel regulation effects, beach protection effects, and influences on river regime, flood control and nearby regions after implementing the two engineering schemes were all comparatively analyzed from water level, velocity, flow direction, braided channel diversion ratio, riverbed erosion and deposition and other aspects. Studies suggest that: after implementing the two engineering schemes, the planned 12.5m channel is continuous, the 500m×12.5m requirement is satisfied with slight dredging; compared with the feasibility scheme, beach protection effects of optimization scheme for Tongzhou Shoal is roughly equal with the feasibility scheme, while for Baimao Shoal, the optimization scheme is better; in optimization scheme, the head of tooth dikes are extended forward, the velocity of shallow areas increased slightly, channel depth improvement effect is better; Langshan Shoal tail submerged dike of optimization scheme can increases the stability of Langshan Shoal tail, and local scouring is decreased. In general, optimization scheme can be the recommend scheme, regulation effects of it are better than feasibility scheme. The relevant results have been used in channel engineering design and decision making.