Balanced scorecard (BSC) is one of the popular performance measure methods which can translate the strategy into a set of clear performance indicators and manage the status of implementing the strategy. However, BSC is unable to simulate the complicated environment, to be short of the strategy's simulation, and is usually used on the business unit level; only a few studies have ever tried to use it on other levels. Therefore, this study tries to combine BSC with SD to explore Taiwan's pharmaceutical industry that had formulated the relevant strategy of development since 1982, but its contribution is still limited at present. Based on four perspectives of BSC, the related indicators will be conducted. Mainly, the purpose of this study is to investigate and build the complex system of Taiwan's pharmaceutical industry, and amend the policy direction to enhance its performance. This paper not only integrates the research tools and gives suggestions to improve the performance of this industry, but also assists Taiwan in becoming a R&D, manufacturing and operations center in the Asia-Pacific region in the future.