In view of two obstacle segments of navigation channel from Taicang to Nantong which were named TZS (Tong Zhou Shoal) Waterway and BMS (Bai Mao Shoal) Waterway, the first phase project of 12.5 m deep-water navigation channel project was designed and now under buliding. The project would make 12.5 m deepwater channel extent from Taicang port to Nantong port. In order to test project effects, movable-bed physical model was designed to optimize layout of the project. TZS sub-project can make obvious effect to prevent shoal erosion, training dike and tooth groins could prevent washing back of left edge of TZS shoal and LSS (Lang Shan Shoal) shoal, erosion development process of scour channel between TZS and LSS could also be prevented. The navigation condition of deep water channel in the east LSS waterway could be improved. BMS sub-project can also make obvious effect to prevent shoal erosion, and change the backward trend of shoal caused by erosion. And also, small sand bar locating in south channel of BMS shoal which cause navigation obstruction was also significantly eroded, navigation condition of the inlet section of south channel of BMS shoal was also improved for the project. In conclusion, the project can achieve the goal of engineering construction.