Microbiology is an important specialized basic course for biology majors in colleges and universities, and it is also the theoretical basis of modern biotechnology. In order to comply with the international development trend and improve the professional English level of college students, more and more universities are implementing bilingual teaching in Microbiology. Cognitive learning theory considers that learners need to form a certain knowledge structure by organizing various knowledge in the learning process, so as to achieve the purpose of learning. This article combines the cognitive learning theory with bilingual teaching of microbiology, and discusses it from three aspects: discovering learning to promote microbiology teaching, contacting with the life to promote meaningful learning, and further improving bilingual teaching in microbiology through learning evaluation, in order to promote the benign development of bilingual teaching of microbiology.