This study aims to find a causal relationship on how the ecosystem affects individual esearchers when producing innovation in a higher education institution. It is filling the gap between existing psychological-based creativity theory and ecosystem-based organization management theory. It also answers the problem of low innovation productivity in higher education institutions by managing the innovation ecosystem. The study uses a qualitative method to find the causal relationships among variables in forming a system using causal loop diagram (CLD). It also uses a quantitative method to measure the effect of the relationships using the stock and flow diagram (SFD) of system dynamics. The post-positivism paradigm with a mixed methodology was used to explain a complex relationship among variables in the innovation ecosystem. The model was built based on theories and concepts available and supported by facts and information taken from previous unpublished research conducted by Thoha and Hutapea (2017) in 5 higher education institutions in Central Java and the hypothesis of the model will be tested and simulated at the University of Indonesia. Conflicting actions and policies to fulfill business goals and government regulation can create unfavorable conditionsfor innovation momentum. Pushing excessiveresearch and innovation targets without giving enough incentives creates a negative reaction from the researchers, fails to create a good work climate and producesa reversing effect on the productivity of innovation. Therefore management must balance their policy with emotional engagement of the researchers.