Abstract: In order to further study the rationality of the pier layout of the Shanghai-Nantong Yangtze River Bridge, some analyses of the influences of the planned bridge on 12.5 m deep-water channel and ship navigation are carried out in this paper. Through the physical model tests, the adaptability and rationality of the pier layout of the proposed bridge are analyzed from the aspects of the hydrodynamic force changes, the riverbed scouring and silting changes, the navigable conditions of the river section at the bridge site, etc.. Comparison of the existing bridge site scheme with the scheme of navigable holes of the main bridge moving 200 m southward is also made in this study. The boat track lines in the river section at the bridge site were measured in the period of the spring tides and the neap tides coming respectively in the dry season and flood reason in April and July, 2010. The research and analysis results show that the existing pier scheme is slightly better when the bridge site scheme is determined, because it can meet the requirements of the actual navigation. And the research results can provide certain theoretical guidance and technical support for the bridge construction in the future.