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The question of how to accelerate innovation is becoming more and more crucial for the pharmaceutical industry to meet the social and economic demand. Complex Products and Systems (CoPS) that is characterized by high cost, intensive engineering and information technology, and many tailored subsystems and components, provides new perspective for improving pharmaceutical innovation. This paper aims to explore the mechanisms of applying CoPS into pharmaceutical research and development (R&D) project. After a theoretical review of CoPS and pharmaceutical innovation, it describes three R & D projects: analysis knowledge, technical complexity of those projects, and decomposition of each. This paper argues that the evolution of pharmaceutical innovation has increased the width demand of knowledge, which makes a feasible and optimal solution for pharmaceutical innovation study and practice.