Objective To establish a quality evaluation system for the medical-engineering integrated education model oriented by innovation ability education and to provide a new paradigm for promoting the reform of medical education. Methods By comprehensively employing methods such as literature analysis, expert consultation, and questionnaire surveys, and leveraging information technology platforms and artificial intelligence (AI) teaching systems, multi-dimensional data including students"" learning behaviors and project participation levels were collected. The weights of evaluation indicators were determined using the analytic hierarchy process (AHP), and an education quality assessment system covering the curriculum system, teaching plans, faculty team, and students"" innovation ability was established. An empirical survey was conducted on 300 medical students from 10 universities. Results Under this model, the average total score of the assessment system was (78.5 ± 5.2) points. Among them, the score of the curriculum system was the highest (82.3 ± 4.1) points, and the scores of students"" innovation ability were all above (73.2 ± 6.1) points. The multiple regression analysis showed that the completeness of the curriculum system, the diversification of the teaching staff, and the richness of the system platform resources were all important factors affecting students"" innovation ability (all P < 0.05). Conclusion The quality evaluation system for the medical-engineering integrated education model oriented by innovation ability education can effectively identify the strengths and weaknesses in medical education, providing reference for the optimization of the medical-engineering integration education model, and promoting the sustainable cultivation of high-quality interdisciplinary medical and engineering talents.