College students are a major force to promote the construction of ecological civilization. Thus, implementing the education of ecological civilization in colleges is an important component for building an ecological civilization society. Microbial Ecology is a discipline in close association with human activities. This article introduces how to implement the education of ecological civilization in classroom teaching of Microbial Ecology by combining the course knowledge points, reforming teaching methods and focusing on daily classroom life. During the process of conveying specialized knowledge, we should strengthen college students’ awareness of conservation, environmental protection and ecology, guide them to practice ecological values and promote the development of ecological civilization in colleges. Meanwhile, this article will provide reference for other related subjects to implement the education of ecological civilization in classroom teaching.