Objective To implement and evaluate the teaching effect of online teaching mode in “endocrine system” integrated course. Methods Totally 156 undergraduates of Grade 2017 8-year clinical medicine program of Shanghai Jiaotong University Medical College joined the research group and carried out online learning from March to June 2020. Totally 142 students of Grade 2016 were assigned as the control group to carry out conventional offline teaching. The teaching effect was evaluated by analyzing online learning data, comparing course scores and questionnaire survey. The independent sample t-test was used to compare the two groups of data. Results All students in the experimental group watched the course video in full and completed their homework after class; The number of posts is 225. There was a significant difference in the total course scores between the experimental group and the control group [ (83.36±8.54) vs. (81.10±7.01), P=0.010], and there was no significant difference in the course final exam scores between the experimental group and the control group [(76.46±13.76) vs. (78.45±10.74), P=0.163]. The results of the questionnaire shown that 32 out of 40 teachers (80.0%) believe that the overall effect of online teaching is similar or better than traditional offline teaching, 106 (76.8%) students in the experimental group were satisfied with online teaching. Conclusions The application of online teaching mode in the endocrine system integration course has achieved good results, and it is basically equivalent to traditional offline teaching mode.