Objective To explore the application of organ-system-based integrated curriculum teaching mode on clinical clerkship of digestive system for eight-year program medical students,thus providing reference for the teaching reform. Methods From September to December 2021, 114 medical students from grade 2018 (58) and 2019 (56) of eight-year program in Peking University Health Science Center were selected as the research subjects joining an integrated teaching mode group and a conventional teaching mode group respectively, A prospective evaluation scale was developed containing five dimensions: initiative, basic medical courses, clinical medical courses, clinical reasoning capacity and medical English level in order to analyze the performance of medical students during clerkship rotation. The paired sample t test was used to compare the normal distribution data between groups. Results In the dimension of initiative, the scores of integrated curriculum teaching mode group were significantly higher than those of conventional teaching mode group [ (25.90±2.56)vs. (21.50±5.34), P=0.030]. The scores of two groups in anatomy and embryology [(8.40±1.08)vs.(6.90±1.52), P=0.020] and medical imaging [(7.70±1.16) vs.(6.50±1.08), P=0.028] in the integrated curriculum teaching mode group were also statistically significant.. In the dimension of clinical reasoning, the scores of integrated curriculum teaching mode group was significantly lower than those of conventional teaching mode group [(20.80±2.25)vs. (24.40±3.95), P=0.022]. In the dimension of medical English level, there was no significant difference between the two groups [(7.50±1.27) vs. (8.00±1.33), P=0.361]. Conclusions The organ-system-based integrated curriculum teaching mode improves learning enthusiasm of medical students and facilitates their mastery of basic and clinical knowledge. However, more attention should be paid to the capacity building of clinical reasoning and communication skill, and medical English education should be fully integrated.