Abstract: Water Treatment Microbiology is a core fundamental course of Water Supply and Drainage Science and Engineering focusing on the study of theories and experimental skills. The theoretical and experimental teaching of this course not only lays the theoretical foundation for students in Microbiology, but also plays an important role in developing students’ innovative thinking and training their practical skills in solving complex engineering problems. On the basis of summarizing the teaching practice of Water Treatment Microbiology in the past 20 years, guided by the goal of New Engineering Construction and the Washington Accord on engineering education accreditation system, insisting on the thought of “student-centered, outcome-based, theoretical teaching reform and experimental innovation integrated, knowledge and practice united”, this paper explores a new teaching reform scheme for improving the students’ ability to solve complex engineering problems, developing their professional innovation ability to meet the new requirements in the field of water supply and drainage under the construction of “new engineering”, and cultivating new application-oriented talents with high quality to meet the needs of the times.