Shanghai-Nantong railway bridge locates at the middle of Chengtong river, a class I chanhnel.The deepwater channel plays an important role to the economy along the stream and the river regime varies due to the influence of Henggang sandbar and Tongzhou sandbar. Thus, the consideration of a variety of channel conditions and shipping transportation for the bridge pier allocation is compulsory. The maximum satisfaction for river transportation could be reached by optimizing bridge pier allocation based on considerations of hydrology,fluvial process, channel condition, shipping transportation, etc.