Graduate students education is high-level personnel trainings. It is the core work in the graduate educations in our country to train the independence and innovation of scientific research abilities of postgraduates. Cultivation of innovative ability is a system engineering, which is based on the innovative experiment teaching methods to train the innovation ability of postgraduates. PBL method is applied to the experiment teachings in the master graduate students depending on the problem existed in the traditional experimental teaching modes for postgraduates. The results show that the comprehensive qualities of postgraduates are significantly improved, including the ability of innovative thinking, problem analysis and resolve, self-learning, experimental operation, and the team cooperation spirit, etc. The practice is a valuable attempt to the reform of the basic medical talents training modes of Nanjing medical university.