Microbiology, as the major course of biological engineering, requires the better practical ability for the students. However, there is obvious problem on a few of comprehensive designing experiment and many proving experiments in the teaching. In order to train the students’ operating ability of basic skills in the microbiology experiments and discovering and solving problems at a higher level, the courses of experiments of microbiology have been adjusted since 2006. The opening comprehensive experiment of “Isolation, Cultivation and Identification of Environmental Microbe” has been added in the courses of the microbiology experiment. The students were asked to search correlative documents and design the experimental protocol independently, and then carried out the experiment with the guide of the instructor. Meanwhile, the comprehensive experiment was incorporated with the innovation match of Yanshan University, which increases the students’ interest and enthusiasm for the experiment. The operational skills of the students have been enhanced significantly. In addition, the abilities of in-dependent solving problems and cooperation in the team have been increased. The excellent teaching result has been achieved with five years’ practice.