In colleges and universities, attention has been paid to smart education, which integrates modern information technology with education and teaching. With the development of “flipped classroom,” remarkable achievements have been made in subject teaching in terms of resource construction, pedagogy innovation and IT support. However, there is still a big gap between the current smart teaching in universities and the core connotation of smart education, in the face of deep-seated questions, such as how to enable students to play the main role in teaching and how to improve their core competence. Deep learning in the field of education, with a capability framework highly consistent with that of smart education, is both a bridge between information technology and smart education and a solution to address the deep-seated questions in the smart education reform in universities. Deep learning can develop students' advanced ways of thinking and the abilities to transfer and apply knowledge, as well as enhance students' advanced cognitive abilities. Therefore, it is necessary for educators to adopt principles of pedagogy oriented towards deep learning, and design smart education from the top to promote the reform of smart teaching in universities.