Environmental Microbiology, one of the basic professional courses, is helpful to figure out environmental issues and to remove engineering roadblocks. Environmental Microbiology was endowed with the support of the national excellent courses and the professional core courses in Zhejiang University. In the course construction process, a new content system was established targeting pursuing the answers of “what are microorganisms”, “what can microorganisms do” and “how to use microorganisms”. A new teaching pattern was proposed, including students lecture, special subject lecture, topic discussion, thesis course and comprehensive assessment. The practice of the new content system and teaching pattern resulted in a good reward, demonstrating the feasibility for the course.