The modular teaching pattern for microbiology experiments helps to improve undergraduates’ experimental skills and their comprehensive application ability. The authors described the construction of the modular microbiology experiment course and its application. First, we established a comprehensive, research-based modular teaching system. The system is composed of three modules including investigation of the environmental microbial diversity; screening and isolation of the special functional microbes, culture conditions optimization and strain improvement; the microbiological testing of water. There were also a total of 12 experimental units. The contents are designed to: (1) Emphasize the training of students in their basic microbiology experimental skills and guide their learning; (2) Strengthen the connection between experiment units and the coherence of different modular experiments; (3) Refine the experimental contents, simplify the experimental steps and reduce students’ study load. Second, we organized the seminars to summarize and gain the experience of teaching, discuss and optimize the following unit plans. These seminars will help us to improve the teaching effect and the teacher’s guidance ability in a microbial experiment course. Third, we established different ways to evaluate the students’ learning, such as routinely reviewing their work for each experimental unit, implementing a practical examination to test their experimental skills at the end of the semester, reviewing their ability to write reports for experimental units, as well as writing for modules in a research article format. All together these will result in better evaluations on the students' comprehensive ability. As an incentive, we will also exhibit the outstanding achievements produced in each of the experimental courses.