Higher education must cultivate a college student’ s innovative ability, practical ability, and entrepreneurial spirit and generally enhance their humanistic quality and scientific literacy. Guided by outcome-based education, we used scientific research projects related to experimental animals and formulated the expected learning output of innovative training projects for college students. We highlighted ability training and strengthened the main status of the students in the project implementation. The results showed that students had an improved self-learning ability, innovation, and practical ability. Scientific research ideas and design of students were systematically enhanced. The concept of experimental animal welfare was also strengthened. Students had quality development in the selection of standardized experimental animals and standardization of experimental operation techniques. In addition, they had the correct understanding and scientific application in theoretical knowledge and key techniques for experimental animals and animal experiments.