Objective To evaluate the online teaching for undergraduates at the pre-medical and basic medicine stage in Peking University Health Science Center during COVID-19 pandemic period and to provide reference for improving the quality of online teaching. Methods Self-designed questionnaire was used in this study. A total of 105 five-year program undergraduates of clinical medicine and eight year program of basic medicine at the education stages of pre-medicine and basic medicine and 10 teachers were selected from February 24 to March 1, 2020.The comparison between online teaching and traditional teaching in terms of strengthens and weakness was implemented. The data were analyzed by Fisher's exact test. Results Compared with the traditional teaching, 37.1% (39/105) of the students and 6 teachers considered that the effect of online teaching was equal to traditional teaching and 39.0% (41/105) of the students and 3 teachers thought that the teacher's in teaching plan document was 125% higher than that in traditional teaching and 35.2% (37/105), 19.1% (20/105), 4.8% (5/105) of the students and 3, 2 and 1 teachers thought that in online teaching environment, the classroom interaction decreased to 75%, 50% and 25% respectively. There was no significant difference between students and teachers in the evaluation of the adequacy of lesson preparation and the effect of classroom interaction (all P> 0.05). Teachers listed three advantages of online teaching as the feasibility of reviewing after class, the teaching time and place were more flexible and the students in different classes were able to join the course simultaneously; Teachers listed three difficulties of online teaching as barrier to implement the training of lab experiment, surgical operation and other clinical skills, the network is sometimes stuck, and students' learning situation were not able to be followed. There were 63.8% (67/105) of the students and 8 teachers thought that online teaching was a complementary pathway for traditional teaching at moment. Conclusions In the online teaching, the teachers are better prepared for the lesson, but the classroom interaction is not as good as that in traditional pathway. The current teaching mode should still be based on traditional pathway and online teaching function as a complementary technology to traditional teaching.