The emerging engineering education is posing a new challenge to the cultivation of professional talents. As the traditional core course of Water Science and Engineering, The Course of water quality engineering is both theoretical and practical, involving a wide range of professional knowledge and comprehensiveness. It is necessary to focus on the connotation of new engineering and national major needs, thus to reform and innovate courses. Aiming at the problems existing in traditional teaching, based on the student-centered approach, to design the multi-level teaching objectives according to ‘knowledge exploration, capacity building, and value guidance’, and to update the teaching contents in line with the latest developments in the industry; to design teaching activities based on the multi-dimensional teaching objectives; to carry out teacher-guided and accompany-style autonomous learning mode; to innovate teaching organization through the adjustment and integration of the sequence of teaching links; to use various classroom forms such as interest experiment introduction, case analysis, classroom debate, flipped classroom, etc.; to assist new information technology; to achieve value guidance by intensifying curriculum ideology and politics; to build a full-cycle systematic evaluation system. The practical application of teaching reform has achieved certain results, which can provide some guidance and reference for the teaching of Water Science and Engineering, Environmental Engineering and other related majors.