As an important platform for the combination of theory and practice, college students' innovative and entrepreneurial training program has an important impact on improving the comprehensive ability of undergraduates. The major of aquatic animal medicine is a new sea-related major. The continuous development and transformation and upgrading of aquaculture in the new period have put forward newer and higher requirements for the innovative and practical ability and comprehensive quality of aquatic animal medicine graduates. Taking the innovation and entrepreneurship program of college students majoring in aquatic animal medicine as an example, this paper analyzes the significance of the innovation training program for college students, the cultivation of students' scientific research ability, and the problems existing in the application and operation of the program, in order to provide a reference for the innovative education and talent training for students majoring in aquatic animal medicine.