Importance: Covid-19 struck the world suddenly and unexpectedly. Since traditional education requires face to face communication, to avoid further spreading of the virus, a majority part of that education has moved online. Objective: Our study attempts to compare the differences between online medical education with a unique course design and traditional face-to-face education. Design: We conducted a retrospectively analysis of a total of 4,098 medical students between 2019 and 2020, including two groups of students who received online education and classroom education of same subjects, respectively. Participants: Freshmen enrolled in September 2018 received traditional classroom physiology and pharmacology education in the spring semester of 2019. Due to the impact of the COVID-19 pandemic, freshmen who were enrolled in September 2019 received online physiology and pharmacology education in the spring semester of 2020. Assessments: The final marks of the two groups of students were recorded and compared. Data on students participating in online discussions, learning, homework, and watching instructional videos were also recorded. Results: There was no significant difference in the final academic performance between the two groups (average mark: 55.93 (online education) vs. 56.27 (classroom education), p=0.488). Further analysis showed that student participation rates in online discussions, online learning, and online viewing of instructional videos were closely correlated with final grades in online courses (p<0.01). Conclusions and Relevance: In conclusion, our results suggested that the pedagogical effects of online education during COVID-19 were promising and we provided a well-designed medical online course to inspire further improvements in online education.