Abstract-Medicinal chemistry is an important specialized course of students majoring in pharmacy and pharmaceutical engineering. In order to improve the teaching effect of Medicinal Chemistry, this article discusses the teaching methods of medicinal chemistry and told how to put the teaching reform into practice. Two methods including traditional way and new method were applied in the different classes. After two years' practice, the students from two classes exhibit different ability in understanding knowledge of medicinal chemistry. The results showed that the new method much better and the students can improve the learning ability in medicinal chemistry course for the students majoring in pharmacy and pharmaceutical engineering.