Influenced by many factors，such as the regulation of upstream and downstream hubs and the project regulation scheme，the channel in the backwater fluctuating section of mountainous river hubs has complex and changeable hydrological conditions.Therefore，determining the design lowest navigable water level has become a key problem.Relying on the waterway construction project from Baishi to Fenshuixi of Qingshui River，the key values of the design lowest navigable water level are determined by a two-dimensional numerical simulation of water flow.It is proposed that the waterway project is designed according to 90% navigable guarantee rate，taking the two most unfavorable conditions of the dry season and the flood season and using the lower envelope of the water level along the route as the design lowest navigable water level.The research results have solved the key problem of the project and can provide a scientific basis for the construction of similar projects.