This article focuses on the research of RTDI policies (research, technology, development and innovation), and the theme of this article is to link the three indicators together: RTDI policy-making process-the contents of RTDI policies-the appropriateness of RTDI policies on the configuration of the national, the sectoral and the technological innovation systems. We define the configuration of the three innovation systems as national, sectoral and technological innovation system (NSTIS). We assume the policy-making process of RTDI policies would shape the contents of RTDI policies. Once the contents of RTDI policies are implemented, the RTDI policies would influence, whether appropriate or inappropriate, on the NSTIS. We use the Taiwanese pharmaceutical biotechnology policies as empirical cases. On the basis of the empirical cases of Taiwan, we find that the consistency and appropriateness of RTDI policies are shaped by four variables: polity, horizontal coordination, vertical coordination and the involvement of external stakeholders. The policy-making process indeed shapes the RTDI policies which further shape the development of NSTIS.