The efforts to improve the function of innovation systems and the exercise of policy instruments for S&T indexes is increasingly recognized as critical to enhancing a country's competitiveness. Despite its great importance for national development, scholars have paid little attention to this policy agenda, in particular to understanding the linkages of national systems, policy instruments, and S&T indexes. In this study, using data from WEF and IMD, we draw on the questionnaire survey and Fuzzy Delphi methods to explore such linkages in Taiwan. We identify the missing linkages in Taiwan's national innovation systems, based upon which policy implications are drawn out. Our study provides insights for new innovation policy instruments that are designed to address the problem of systems of inertia.