Paper presented in the AEA 2014 Conference held in Denver. Comparing and utilizing the evaluation framework for S&T program performance indicators employed by the United States, Canada, South Korea, etc., we tried to restructure Taiwan’s current indicator system based on the clear logic model to reflect the science production system structure and agency’s mission, respond to societal needs by targeting the clients and the outcome for the targeted clients, capture the delivery network and the intangible Triple-Helix interactive benefits, assure the correspondence of monitoring indicators to the scheduled evaluation methods, and thereby determine what to measure, when to measure, and how to interpret the measurement outcome.