Cultivating the top-notch innovative talents is an essential task for connotative construction of higher education. As an application-oriented discipline, the Discipline of Food Science and Engineering attaches great importance to the cultivation of innovation ability of college students. For a long time, however, the discipline education has problems of the inverted teaching subject position, weak coordination ability and single practice mode. The support for the cultivation of innovation ability is weak and ineffective. Therefore, in the context of professional certification of engineering education, it is necessary to make reform of traditional education mode and improve the carrier support and target acquisition taking the Outcomes-based Education (OBE) as guide, the innovation ability cultivation as objective, to provide effective guarantee for cultivation of the top-notch talents. These have become issues that should not be ignored in the development of the Discipline of Food Science and Engineering.