The pharmaceutical industry is characterized by the intensive capital and knowledge. Its international competitiveness and sustainable development should be established on a complete national drug innovation system. At the same time, the development of new drug innovation system in China can be really promoted by the accurate location of pharmaceutical enterprises as research and development (R & D) and production, the improved R & D strength, as well as the increased investment in innovation. This paper reviews both the development of Chinese drug innovation system and the orientation of pharmaceutical enterprises innovation during this process. Furthermore, the changes of innovation capability and positioning of pharmaceutical companies have been investigated before and after the launch of the Drug Innovation Major Project. Although, the construction of Chinese pharmaceutical innovation system has greatly promoted the progress of our pharmaceutical companies, a wide gap in the level of drug innovation still exists between Chinese pharmaceutical enterprises and international leading drug companies in the world.