Abstract Green environmental protection is the trend of social development, and the cultivation of green ideology and corresponding skills are becoming the responsibility of education. Medicinal chemistry is one of the core courses of pharmacy major in high vocational education. In this paper, the twelve principles of green chemistry were set to be the main line of teaching medicinal chemistry combined with multiple living examples applied the philosophy of green chemistry and its implementation method to the drug structure design and process route. This way promoted students' understanding of the twelve principles of green chemistry, and enriched their green chemistry experiences and skills within the area of pharmaceutical sciences.