Objective To explore the effect of the integrated teaching model of theory and practice based on outcome-based education (OBE) in clerkship teaching of digestive system. Methods A total of 134 5th-year undergraduate students major in clinical medicine from Binzhou Medical University and in clinical clerkship in Department of Gastroenterology and Hepatology of Binzhou Medical University Hospital were selected from November to December 2021. They were divided into two groups by class, with 64 students in the experimental group and 70 students in the control group. The experimental group adopted the integrated teaching model of theory and practice based on OBE principles, while the control group adopted classroom and clinical internship learning in learning digestive system. Both groups took a comprehensive examination before and after the class, and the experimental group was given a post-course questionnaire on teaching effects. T-test was used to analyze the data. Results At the end of the course, the progress of the experimental group was higher than that of the control group (86.18±8.64 vs. 75.00±6.92, P<0.05). Theoretical knowledge and clinical comprehensive scores of the experimental group were higher than those of control group (43.38±7.50 vs. 38.79±7.49, 42.79±6.60 vs. 36.21±7.78, P＜0.05). The results of the questionnaire showed that students in the experimental group were satisfied with the instructional design, participation, and evaluation, with values of (3.30±0.55), (3.11±0.62), and (3.20±0.59). Conclusions The integrated teaching model of theory and practice based on OBE principles is conducive to the mastery of theoretical knowledge, the development of integrated clinical competencies, and active participation in learning among medical students. It has also been recognized by students for teaching design and assessment.