OBJECTIVE： To study the innovation system synergies of pharmaceutical manufacturing industry in Shanghai and lay the foundation for further enhancing the competitiveness of pharmaceutical enterprises of Shanghai. METHODS： Based on the composite system synergy degree model， order variables （G） of innovation environment （S1）， innovation technology research and development （S2）， innovation technology absorption （S3） and innovation output （S4） in the pharmaceutical manufacturing industry innovation system in Shanghai during 2006-2014 were selected， synergy degree model was built， and order parameter， order degree， synergy degree of each order variable were calculated in turn. RESULTS & CONCLUSIONS： S1-S4 obtained 4， 4， 4， 2 order variables respectively. According to the calculation， synergy degree of pharmaceutical manufacturing industry in Shanghai during 2006-2014 ranged in －0.195-0.202， average value was －0.068， overall in the level of “inverse synergy” and “non-synergy”. Thus， the internal development of the pharmaceutical manufacturing innovation system in Shanghai is more disorderly. It is suggested to reform from the two core influencing factors of the stability of innovative environment and promoting technology absorption， including accelerating the transformation and upgrading of the pharmaceutical industry to create a stable and innovative environment， increasing the innovation investment of the pharmaceutical industry to improve the level of technology absorption and independent innovation， as well as strengthening cooperation within and outside the domain to effectively enhance the system synergy degree level of pharmaceutical manufacturing innovation system in Shanghai.