In response to the requirements for medical talent training set out in Healthy China 2030, this study addresses the issues of inadequate adaptation between traditional medical education and smart learning, as well as the fragmentation of learning engagement empowerment mechanisms. Drawing on theories such as NSSE-China, we analyzed the current status of smart learning engagement in medical education and constructed an empowerment mechanism through a questionnaire survey (n = 520) and in-depth interviews (n = 30). The results showed that the average score of smart learning engagement in medical education was 2.84 (slightly below moderate), with issues including dimensional imbalance, group differences, and dislocation of teachers’ and students’ perceptions. The verified “cognitive-behavioral-emotional-environmental” four-in-one empowerment mechanism increased learning engagement in the experimental class by 24.6%, and the academic performance and higher-order abilities of students in the experimental class were significantly superior (P < 0.01). This study provides a scientific scheme for the intelligent reform of medical education.