MOOCs is a new education mode which by using the Internet to transmit the curriculums to the world to gratified the desire and the pursuit of people. In addition, it's not only an important way to accomplish convenience and mobility of study, but also a study way put emphasis on scenario and sharing. This paper will use the MOOCs and Flipped Classroom to design the teaching resources of evidence-based medicine. By combining the teaching content and characteristics of evidence-based medicine with the successful experience of the existing MOOCs, we make a teaching mode of the evidence-based medicine which is based on the students' autonomous learning and flipped classroom. And the practice of the MOOCs of evidence-based medicine will according to this mode in the future.