Agricultural Microbiology is a specialized basic course in agricultural colleges and universities. With the rapid development of microbiology, the reform of traditional teaching concepts and methods is not only to meet the needs of the times, but also an inevitable trend of historical development. This paper explores the reform of the teaching process of agricultural microbiology from the following aspects: the reform of teaching materials, the expansion and extension of experimental teaching contents, and the change of teaching consciousness and ideas. The purpose of the reform is to better promote the cultivation of students’ innovative ability, so as to build a first-class socialist university with Chinese characteristics.