In view of two obstacle segments of navigation channel from Taicang to Nantong named TZS (Tongzhou shoal) waterway and BMS (Baimao shoal) waterway, the first phase project of 12.5 m deep-water navigation channel project was designed and now is under building, aiming at extending from Taicang to Nantong port. In order to study project effects, movable bed physical model is designed to optimize the project layout by comparing normal-rainfall-sedimentation-two-years and rich-rainfall-sedimentation-year conditions. TZS subproject has obvious effect to prevent shoal erosion, training dike and tooth groins can prevent washing back of the left edge of TZS and LSS (Langshan shoal), and the erosion development process of scour channel between TZS and LSS can also be prevented. The navigation condition of deep water channel in the East LSS waterway can be improved. BMS sub-project also has obvious effects to prevent shoal erosion as well as to change the backward trend of shoal caused by erosion. Also, small sand bar locating in south channel of BMS which cause navigation obstruction was also significantly eroded due to the projects, navigation condition of the inlet section of south channel of BMS was also improved. Conclusions can be drawn from the study that no obvious difference can be seen between the tests under normal-rainfall-sedimentation-two-years condition and rich-rainfall-sedimentation-year condition. Overall,the project can achieve the goal of engineering construction.