Abstract: Based on the perspectives of technology innovation value chain and complex systems theory, the Chinese pharmaceutical industry technology innovation system can be deconstructed into four subsystems of internal technology R&D, external technology acquisition, commercialization and innovation supporting environment, to understand the evolution state and rule of this system. Using the data of statistical yearbook from 2007-2015 and the synergy degree model of composite system, this system’s synergy degree and its subsystems’ ordering degree in the evolution process are measured and analyzed. The results show that this system’s overall synergy degree and its subsystems’ ordering degree show a dynamically rising trend as time goes on but their average values are low; technology external acquisition subsystem is the restriction factor for the synergy development of the whole system to the high level; the influencing weights of different order parameters on their respective subsystems’ ordering degree are different; the significant polices for China’s pharmaceutical industry may produce a clear short-term effect on the system’s synergy development. Finally, some policy recommendations are made based on the above conclusions.