Objective To analyze the current status and challenges of medical students′ participation in the innovation and entrepreneurship training program (IETP) and propose optimization strategies. Methods From October 2024 to June 2025, 117 medical students and 4 supervisors from Chongqing Medical University were selected using cluster sampling and stratified purposeful sampling. Data regarding participation motivation, project implementation, research skill enhancement, and difficulties were collected via self-developed questionnaires and semi-structured interviews. Results The primary motivations were enhancing competitiveness for further education [107 (91.5%)] and achieving research outputs [84 (71.8%)]. In total, 98 (83.8%) projects were finalized by students through literature reviews based on research frameworks provided by supervisors. All 117 (100.0%) students spent at least one hour daily on their projects, mastering various experimental skills and improving comprehensive research capabilities. The main obstacles were insufficient research time [98 (83.8%)] and technical learning difficulties [84 (71.8%)]. Conclusions While the IETP helps stimulate students′ initiative and cultivate their comprehensive research capacity, however, several problems remain, including insufficient research time, difficulties in mastering experimental techniques, an imperfect assessment system, and strong utilitarian motivations among students. Future improvements should be made in reasonably optimizing curriculum schedules, providing research skills training, establishing a tripartite assessment mechanism involving universities, supervisors, and students, and offering dedicated political and virtuous awareness courses for innovation and entrepreneurship.