With the development of the construction of New Agricultural Sciences, animal medicine majors have entered a new stage of educational reform. Colleges and universities should adhere to the basic goal of “fostering virtue through education and strengthening agriculture to revitalize agriculture”, conduct an in-depth analysis of the reform needs of the Veterinary Microbiology course in terms of interdisciplinary integration, practical reform, and the integration of ideological and political education into courses. On this basis, they should promote the update of teaching content, the innovation of teaching methods, the reconstruction of the experimental teaching system, and the optimization of the assessment and evaluation mechanism, to create favorable conditions for the cultivation of compound talents in animal medicine majors. Against this research background, this paper expounds the requirements put forward by New Agricultural Sciences for the teaching reform of Veterinary Microbiology, summarizes the reform dilemmas faced by the teaching of Veterinary Microbiology, and proposes the teaching reform strategies of Veterinary Microbiology under the background of New Agricultural Sciences, to provide support for colleges and universities to cultivate outstanding talents with both professional capabilities and feelings for agriculture, rural areas and farmers.