With the rapid development of multimedia technology, the student centered flipped classroom model (FCM) and massive open online courses (MOOCs) have been increasingly introduced and implemented in higher medical education. However, comparative analyses of the offline face-to-face FCM and completely online FCM have been rarely reported. In this study, we focused specifically on a set of flipped classrooms in which prerecorded videos were provided before class. Using the Zhihuishu platform as the major online course platform, our team built a MOOC and evaluated the teaching effectiveness of the FCM in both the offline face-to-face class and the online electronic live class for medical genetics education. Questionnaires, paper-based and oral exams were used to collect data on the teaching effects of the different teaching methods. We found that student satisfaction and overall student performance in the offline FCM group was significantly higher than that in the completely online teaching group. Although online FCM allowed students to play back and review anywhere and anytime after class, students taught in offline FCM had a significantly higher degree of knowledge mastery, had a deeper understanding of theoretical knowledge, and were better at knowledge comprehensive application. The effects of their training on genetic disease clinical diagnosis and treatment skills were significantly better, and their capacity for scientific research was also significantly improved. Our research discussed the advantages of the online courses and the problems brought about by using these technologies, and it provided insight into online teaching practices in the era of internet-based medical education.