The excellent engineer training program in water supply and drainage science and engineering aims to cultivate excellent talents who can meet the needs of national strategies and industry development in the context of ecological civilization construction. This paper takes the water supply and drainage science and engineering major of Huazhong University of Science and Technology as an example to analyze the outstanding problems existing in the early training process of excellent talents in colleges and universities, such as insufficient integration with major national strategic needs, difficulty and depth of courses that need to be improved, insufficient cross-disciplinary research, relatively insufficient engineering practical ability, and the all-round talent training system is not sound enough. To deal with these problems, we have carried out the reform, innovation and practice of the training system, including the integration of ideological and political elements into the curriculum teaching to closely combine the major national strategic needs, following the training goals of excellent talents to improve professional challenges, depth and breadth, focusing on discipline frontier and interdisciplinary to improve students’ comprehensive abilities in innovative research, reporting and summarizing, and independent learning, strengthening practical teaching to build a three-dimensional integration engineering innovative environment talent training mechanism, and accelerating the creation of scientific research infrastructure platforms such as the comprehensive innovation experimental platform for water treatment and the virtual simulation experimental teaching platform to comprehensively improve the quality of the whole process and all-round training of talents. Through practical testing and industry evaluation, the excellent engineer training system has obvious innovative features and remarkable results. Students’ academic achievements has increased by more than 10% on average, teacher-student interaction has been strengthened, and students have achieved a series of innovation and entrepreneurship achievements including the SZWG Cup and Challenge Cup. Employers’ comprehensive satisfaction rate for graduates of this major reaches 100%. The teaching reform achievements have won many provincial and ministerial awards, which has a certain degree of promotional and reference value.