The pharmaceutical industry is a capital driven industry and is heavily dependent on R&D for new products and growth in a globalized economy. Since the 1980s, the Taiwan government has recognized that the pharmaceutical industry is important for Taiwan's future development, so the government has formulated national institutions to foster and innovate the development of the pharmaceutical industry. However, previous studies suggested that the innovation of Taiwan's pharmaceutical industry is incomplete. To address the problems and a uncover potential solution from a systematic perspective, this study aims to propose a multi-level framework consisting of national, sectoral and technological views for analyzing Taiwan's pharmaceutical industry. The framework allows providing the landscape of Taiwan's innovation capability in the pharmaceutical industry as well as systematically understands the interaction among government regulations, university researches, industrial evolutions, and market developments.