With the implementation of the fundamental task of “establishing morality and cultivating people”, the construction of the pattern of “Great Ideological and Political Education” has become an important measure for colleges and universities to promote the concept of “all-round education, whole-process education, and all-staff education” at present. In this process, teachers should deeply grasp the characteristics and advantages of ideological and political education in courses, realize the goal of ideological and political guidance through the integration of ideological and political elements with professional courses, and gradually build a pattern of “Great Ideological and Political Education” featuring “full participation, whole-process implementation, and all-aspect fulfillment.” This paper explores the course of Medical Microbiology, expounds the problems faced by the teaching of Medical Microbiology in colleges and universities under the pattern of “Great Ideological and Political Education”, and then puts forward the paths and strategies for the curriculum reform of Medical Microbiology in colleges and universities under this pattern. In this way, it organically integrates value shaping, knowledge impartment, and ability cultivation, realizes the parallel development of the Medical Microbiology course and ideological and political education, and provides strong support for cultivating outstanding medical talents with both virtue and ability, as well as noble medical ethics in the new era.