Objective Exploring the impact of the tutorial system combined with peer teaching in the ″independent design experiment″ module of medical functional experiment on the scientific research innovation ability of medical undergraduates. Methods A self-controlled study was conducted from September to November 2023, involving 84 eight-year clinical medicine students from the class of 2020 at Peking Union Medical College. The tutorial system combined with peer teaching was implemented. Tutors evaluated the experimental design proposals twice—before and after the course—and a student questionnaire survey was administered to assess the impact of this teaching approach on the scientific research innovation ability of medical students. Data analysis was performed using t-tests and χ² tests. Results Through the implementation of the tutorial system combined with peer teaching intervention, students showed significant improvements in various aspects, including the difficulty and novelty of the research topic, the rationality and rigor of the experimental design, and the statistical analysis of the results [(68.00 ± 2.96) vs. (89.00 ± 3.92), (66.00 ± 5.01) vs. (88.00 ± 4.31), (67.00 ± 4.56) vs. (91.00 ± 5.01), all P < 0.001], with statistical significance. Among the 84 medical undergraduates, 90.48%(76/84)agreed that the tutorial system combined with peer teaching effectively addressed the difficulties they encountered during the experimental design process. Conclusions Implementation of a combined tutorial-peer teaching approach in the ″Independent Experimental Design″ module of Medical Functional Experiment Courses significantly enhances scientific research innovation capabilities among medical undergraduates.