Medicinal chemistry, as the core curriculum of the pharmaceutical engineering major, contains complex knowledge systems and scattered knowledge points. A medicinal chemistry course covers more than 50kinds of drugs divided into 11 categories including antibiotics, antiparasitic drugs, anesthetics, nonsteroidal anti-inflammatory drugs, and nervous system drugs. This places a substantial learning burden on students and seriously affects their learning interest and initiative. On the basis of the innovative curriculum reform of "student-centered" learning and with the aim of improving the quality of instruction provided in medicinal chemistry courses, a novel "student-centered team-based learning" (SCTBL) method was developed to cope with these challenges on the basis of our long-term teaching experience. This paper introduces the essence of the team-based learning method and explores the application of SCTBL in the process of teaching medicinal chemistry, which consists of three stages: preclass, in-class, and postclass. The results show that introducing the SCTBL method into medicinal chemistry instruction is conducive to improving students' learning enthusiasm and initiative, which is of great significance to the development of medicinal chemistry education.