To solve the problem of channel route selection for the project connecting the water systems and canals in Hunan Province and Guangxi Zhuang Autonomous Region，this paper systematically summarizes the project’s characteristics and route selection principles and proposes four feasible route schemes.By means of qualitative analysis and quantitative calculation，the paper systematically compares the factors of each route，such as navigation efficiency，water supply conditions in watershed sections，navigation-obstructing facilities，and ecologically sensitive targets.The results show that Route 1 can serve as a recommended route for the Hunan-Guangxi water transportation passage as it has many advantages，such as high navigation efficiency，low elevations in watershed sections，favorable water supply conditions，and no reconstruction of high-speed railway bridges.