College students' innovation and entrepreneurship training programs are an important measure for education reform in colleges and universities, and the initiation program has become an important part of the undergraduate education system for medical students. To assess its effectiveness in enhancing the overall competence of clinical medical undergraduates, This study investigated and analyzed 64 eight-year undergraduates in clinical medicine in innovative training programs in Peking University Health Science Center enrolled from 2018 to 2021 by questionnaire. The results showed that the innovative training program contributes to the improvement of students' literature retrieval ability [39(60.9%)], paper writing ability [37(57.8%)], basic scientific research ability [30(46.9%)], clinical research ability [36(56.3%)], and teamwork ability [42(65.6%)]. However, the work performed by students in the program is relatively single, mainly focused on literature review [61(95.3%)]. Therefore, suggestions and considerations for further optimizing the innovation project are proposed: providing detailed program backgrounds and research content, selecting programs and offering scientific research training courses, adjusting the setting of the innovative training program in combination with the fostering proposal, and establishing a “mentor-student bidirectional” evaluation system.