Pharmaceutical Integrated Experiment (PIE) is a systematic and comprehensive compulsory course for undergraduates majoring in pharmacy and pharmaceutical engineering. This course mainly focuses on integrating the theoretical knowledge of various disciplines into practice, enabling students to master the key processes of drug research and production. In view of the shortcomings of traditional PIE teaching in many domestic colleges and universities, we adopted teaching reform and exploration in 2021 and 2022. Specifically, based on our experience in development of novel SIRT5 inhibitors, we presented a project-based teaching model and selected "Design, Synthesis and Biological Evaluation of Potential SIRT5 Inhibitors" as a case to implement such teaching model. In our course, students worked in a small group to participate in seven interrelated course segments. Throughout the course, we paid attention to process assessment and students' multirole participation in course. We effectively combined the student's course grades and survey results to evaluate students' overall learning effect. Compared to traditional PIE course teaching, this project-based PIE course teaching model is more likely to stimulate students' enthusiasm for self-directed learning due to the more continuous and permeable experimental content, thereby effectively improving the teaching quality of PIE courses.