There are many shortcomings in the experiment course of Environmental Microbiology, such as the less practice on experiment skills, no relationship between the designed contents and scientific researches, and sometimes the valued experiments were ignored. Therefore, changes should be done urgently. In this paper, the current status and problems in the experiment course of Environmental Microbiology were totally analyzed. The comprehensive experiments were designed aiming for scientific research innovation and scientific research goals. The inovation idea was that experimental teaching results should be converted into scientific research pre-production. Moreover, in order to improve the experimental skills and creativities, the specific directions and methods of the teaching innovation was mainly discussed.