Objective To explore the effect of online teaching for stomatology and to analyze the existing weakness of online teaching, so as to provide reference for improving quality of online teaching. Methods Data analyze method was applied in this study, and the examination performance of eight major courses in the second semester of senior undergraduates of stomatology major in Peking University Health Science Center enrolled in 2015 and 2016 and the performance of learning by undergraduates enrolled in 2016 were selected as the research objects. Students of enrolled in 2016 adopted online teaching supported by “Chaoxing Xuexitong” Learning Platform, while students of enrolled in 2015 adopted traditional classroom teaching method. Results Among the 8 courses, except for 6 courses with less practical operation, scores of more practical operation courses such as prosthodontics of undergraduates enrolled in 2016 were lower than that of undergraduates enrolled in 2015 [(77.69±11.28) vs. (82.02±4.42)] and periodontology [(75.76±10.95) vs. (83.17±5.94) ], and the differences were statistically significant(all P＜0.05). The completeness of learning process during the first four weeks of undergraduates enrolled in 2016 was 44.3%(27/61), and it reached 100.0%(61/61) in the eighth week after feedback and supervision from teachers. Conclusions The effect of online teaching for stomatology courses based on multiple practical operation was not as good as the traditional offline teaching method, while the effects of stomatology courses learning which need less practical operation do not show significant difference between online and offline teaching.