The rapid development of life science and biological industry puts forward higher requirements on the cultivation of students’ practice ability and innovation ability. In order to improve the practice ability and research innovation ability of biotechnology and biological engineering students, we carried out the research-based designing experiments teaching reform in Microbiology experimental courses. In view of the content characteristics of the research-based designing experimental project and the common problems in the teaching process, we summed up a set of relatively perfect way of teaching design and process management. The 12 years of practice shows that the research-based designing experiment teaching has a significant effect on promoting students’ professional learning and carrying out their practical ability and research innovation ability. Research-based designing experiment teaching is a new teaching mode with promoting significance.