The Excellent Engineer Training Program of Water Supply and Drainage Science and Engineering aims to cultivate excellent talents who can adapt to the national strategy and industry development needed for the 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 address the outstanding problems existing in the early training process of outstanding 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, closely combining the major national strategic needs, improving professional difficulty, depth and breadth, following the training goals of excellent talents, and focusing on disciplines frontier and interdisciplinary to improve students' comprehensive abilities such as innovative research, reporting and summarizing, and independent learning, and strengthening practical teaching, building a "three-dimensional integration" engineering innovative environment talent training mechanism, 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, comprehensively improving 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 performance has increased by more than 10% on average, teacher-student interaction has been strengthened. 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 professional teaching reform achievements have won many provincial and ministerial awards, which has a certain degree of promote reference value.