Objective: Pharmaceutical chemistry plays a key role in pharmaceutical speciality, which is aiming at making students master basic concepts, basic theory and basic skills of pharmaceutical chemistry. The teachers, however, often encounter some challenges in their teaching process, such as insufficient learning motivation for students, lack of effective means to achieve teaching goals, non-uniformity of program outcomes and ability to satisfy industry needs. It is necessary to seek for an efficient way to improve teaching level by applying new mode. Methods: In view of the great success of Problem Based Learning (PBL) mode in medical courses, this mode is also attempted in pharmaceutical chemistry. We applied PBL method in teaching of pharmaceutical chemistry with the procedure as follows: Under the guidance of teachers, students carry out an active learning around the core knowledge or problem in each module, undergoing a logic process of "asking questions, establishing hypothesis, self-study to disambiguation, demonstrating hypothesis" to acquire knowledge. Results: Well-design of curriculum program and reasonable setting up of assessment system are both emphasized in teaching reform. Through teaching reform of PBL mode in pharmaceutical chemistry, complicated materials are easily to understand and basic knowledge is easily connected to practice. In addition, students' enthusiasm of autonomous learning is inspired and good teaching effects are found. Conclusion: Only more efforts in teaching practice in pharmaceutical chemistry are unceasingly made, will the goal of teaching reform with PBL method be achieved.