Purpose: To explore and analyze the effectiveness of the problem-based learning (PBL) model in clinical gastroenterology education. Methods: This study involved 40 postgraduate gastroenterology students from January 2020 to December 2021, who were randomly assigned to two groups using the random number table method: a control group (n = 20) receiving conventional teaching and a research group (n = 20) receiving the PBL model. The teaching outcomes of both groups were compared and analyzed. Results: The research group exhibited significantly high scores in both theoretical and practical examinations compared to the control group (P < 0.05). Moreover, the satisfaction levels of the trainees in the research group with the teaching model were significantly greater than those in the control group (P < 0.05). Conclusion: In the realm of clinical gastroenterology education, the PBL model proves to be an effective method for enhancing the theoretical and practical performance of postgraduate trainees. Furthermore, it garners high levels of satisfaction among students, underscoring its clear clinical value.