Objectives The value education in the course of Animal Microbiology was effectively conducted to realize a high integration between molding value, training ability, and imparting knowledge. Methods The objectives of value education in the course of Animal Microbiology were formulated based on the requirements from the industry, the purpose of the education, the characteristics of the course and the guidelines for value construction in the colleges and universities. A teaching team of value education in the course of Animal Microbiology consisted of full-time teachers aged at senior, middle, and junior on campus, enterprise practice instructors, industry experts, and teachers of value education courses was established. The "Four Integration and Five Body" teaching mode of "on-the-job course competition, certification and value education" was conducted to educate students in terms of all staff, all aspects, and the entire process. The student centered, teacher led, and value education integrated online and offline blended teaching was practiced. The effectiveness of teaching was multiply evaluated after class. Results The reform of value education in the course of Animal Microbiology achieved remarkable results in practice. The employment rate of graduates reached 99%. The teaching team originally developed the digital resources for the elite online course named as "Job-Course-Competition-Certificate-Thinking". Students won many awards in the National Skills Competition, the Beijing Youth Innovation Competition, the "Challenge Cup" Capital Undergraduate Innovation and Entrepreneurship Plan Competition, and the China International "Internet plus" Undergraduate Innovation and Entrepreneurship Competition in recent three years. Conclusions The value education in the course of Animal Microbiology realized the high integration of imparting knowledge, training ability, and value driven, which improved the effectiveness of education and enhanced the quality of training talent.