Abstract This paper proposed PBL-CBL-Seminar three-dimensional teaching mode of medical organic chemistry, in which clinical cases as the carrier, problems as orientation and discussion papers as medium. This teaching mode realized the transition from CBL to PBL, then to seminar. Moreover, the differences of the teaching-reform class and the control class could be obviously reflected by questionnaire and teaching quality evaluation. The test results showed that the average score of the students in teaching-reform class was as high as 88.9, having good teaching effect, and the novel teaching method could inspire the students' learning interests, cultivate their innovative thinking mode, enhance the consciousness of teamwork, and establish a stable foundation for cultivating extended type talents in clinical medicine.