The Zhajiao reach is a typical branching reach in the upper Yangtze River，which has low water obstruction to navigation of curving and shallow water channel with a high velocity. Based on the navigational characteristics，the regulation scheme of navigation by two branches is put forward. By a combination method of physical model experiment and two-dimensional numerical model calculation of water and sediment，the characteristics of water flow and sediment transport before and after excavation are analyzed. While excavating the new channel，the left branch diverges obviously，and the flow pattern in the beach mouth is improved. The new channel becomes the main transport path of sediment with the increase of the coming flow，and there is little sediment deposition. Meantime the bed load movement of pebbles meets the law of flood-silting and dry-scouring balance within a year，and the two branching channels stability is good.