National policies for science parks and innovation have been identified as one of the major driving forces for the innovation-driven economy, especially for publicly funded science parks. To investigate this collaborative ecosystem (government-academia-industry) for growth and sustainable development, this paper proposes a nation-wide economic impact analysis of science parks and innovation policy based on historical data drawn from one of the globally recognized high-technology industrial clusters in Taiwan. Systems thinking with causal loop analysis are adopted to improve our understanding of the collaborative ecosystem with science park policies. First, from a holistic viewpoint, the role of government in a science parks and innovation ecosystem is reviewed. A systems analysis of an innovation-driven economy with a science park policy is presented as a strategy map for policy implementers. Second, the added economic value and employment of the benchmarked science parks is evaluated from a long range perspective. Third, the concepts of government-academia-industry collaboration and policies to innovation ecosystem are introduced while addressing the measures and performance of innovation and applied R&D in the science parks. We conclude with a discussion of lessons learned and the policy implications of science park development and an innovation ecosystem.