Environmental Microbiology is an important professional course for environmental specialty undergraduates. In view of the practical problems that affect teaching effect in the traditional teaching process, an innovative teaching mode is developed by introduction small private online course (SPOC) and Problem orientation into Environmental Microbiology using the intelligent tools of Rain Classroom. This blended teaching mode mainly consists of three parts: production of online teaching content, teaching implementation and effectiveness assessment, evaluation and feedback. This blended teaching mode takes into account the psychology of the students. Problem-oriented teaching can fully stimulate students’ interest in learning, giving students more personalized experience and enhancing the interaction between teachers and students. Thus, the preliminary exploration showed that the innovative teaching mode of SPOC and Problem orientation can effectively improve the teaching quality and effectiveness by improving teaching process. The blended teaching mode helps to cultivate innovative talents in the field of environmental protection with professional knowledge and skills of environmental microbiology. It can also provide a reference for improving the teaching quality and effectiveness of other courses.