Innovation ecosystems are classified as one of the complex economic systems where many parties with different interests are involved. The holistic objective of such alignment of entities is to cooperate in the creation of innovative outputs. The innovation ecosystem provides the environment for large corporates, entrepreneurs, investors, and governmental institutions to accumulate their sole offering into value capturing via networking and exchanging knowledge and expertise. Thus, such kind of ecosystem exhibits multiple partnerships and interactions among actors to fulfill their own needs and contribute to the value co-creation process. This paper explores the nature of innovation ecosystem as a set of networks comprising a large spectrum of agents interacting with each other. Most of the previous work on ecosystems has pursued qualitative studies emphasizing on how to orchestrate an innovation ecosystem entirely. However, we addressed such a phenomenon by means of an agent-based modeling considering both the micro level of the system which consists of the individual agents and the macro level which is represented by the aggregating of individuals’ behaviors. The model can be used as a decision-making tool to examine the validity of an orchestrating strategy by detecting its dual impact on individual agents and on the overall performance of the ecosystem.