In recent years，ports and harbours have been developing rapidly and riverside industrial zones booming alongside the Changjiang River in Jiangsu province，which poses new challenges for the main channel of the downstream Changjiang River.As a result，it is proposed to execute a channel regulation project in the Lower Reach of the Changjiang River downstream of Nanjing，to deepen the main channel of the said lower reach from 10.5 m to 12.5 m.There lie several branched waterways in some parts of the lower reach downstream of Nanjing.Therefore，the selection of the branch for the main channel will not only determine the overall pattern of the Changjiang deep-water channel，but also have a significant influence on port operations and development alongside the branched river reaches.Considering the requirements in technical feasibility，harbour suitability，traffic management，etc.,this paper presents some essential principles on the selection of branch for the main channel in a branched reach of a river.Fujiangsha reach is the only section of the lower reach which has three branches of waterways.Based on an analysis of the stability of its branches，this paper gives four potential categories of options for branch selection.Mathematical models and other methods are used to analyze their possible effects and influence to get one feasible option from each category of options respectively.Through demonstration in all aspects according to the proposed principles on the branch selection，two options，separately selected from “Fuzhong two-way” category of options and “Fubei one-way+Fuzhong one-way” category of options，are recommended for further analysis in the next stage.