The paper studies the effective, strategic and sustainable interaction between start-ups, venture investors and corporations occurring within the course of innovation investments; it analyses some results of merger and acquisition processes. When modelling these interactions between the entities of innovation ecosystems the authors used agent-based method as the most applicable for decentralized system modelling which also includes the venture investment sector and the merger and acquisition market. Modelling various case scenarios for government regulator, the authors propose some cases and sustainable solutions which enable the overall growth of economy and lead to the optimization of inputs and outputs and to the systematization of the model.