As the most important water resources allocation project in China, the South-to-North Water Diversion Project has been bringing great economic, social and ecological benefits to China via the First Phase of its Middle and East Routes. In the new era, the national development strategy, high-quality development and ecological civilization construction have posed higher requirements for the construction and development of the South-to-North Water Diversion Project. We analyzed and summarized the major achievements of and challenges as faced with the project, and discussed the ideas of water resources allocation which adapt to high-quality development and ecological civilization construction. Last but not the least, we put forward measures to boost the ecological benefits of the Middle and East Routes and suggestions of scheme comparison for the West Route.