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This paper evaluates prospective technology areas, development strategies, and various innovation resources in China's pharmaceutical sector through the use of a hierarchical decision model. The results indicate that although domestic SMEs are the major preferred innovation alternative, it is followed closely by foreign MNCs. The sensitivity analysis indicates that the effectiveness of policy decisions are influenced by certain high technology areas. Recombinant therapeutic proteins, recombinant vaccines, and monoclonal antibody technologies are identified as the major areas that will influence the priority of innovation resources. The research crafts a research framework to formulate innovation strategies in dealing with the uncertainties of technology development and policy decisions in the biopharmaceutical industry.