On the basis of the channel conditions and the analysis of the riverbed evolution of Bagua island in the downsteam of the Yangtze River, we calculate specifications of the special two-way navigable waterway of Baota, and carry out the waterway optimization design and adjust scheme design for the navigation marks. The adjustment satisfies the demands of two-way for different types of ships, and the development demand of the enterprises along the Yangtze River. In addition, it provides a foundation for the long-term development of this channel.