In this paper, criteria for the distribution of stakeholders of the innovation ecosystem (IE), such as subsystems, functional features and positions, are formed. Stakeholder matrices and maps have been constructed for monitoring and identifying trends in changes in the rank of stakeholders in the innovation ecosystem. According to the conducted calculations, in addition to quantitative calculations, their qualitative assessments were provided according to linguistic sets. In the process of research, the method of constructing membership functions of discrete fuzzy sets, as cognitive modeling, was used to determine the influence of cause-and-effect relationships. The elements of the matrix of mutual influences of the cognitive map were expertly formed in the modeling process. The purpose of the paper is to identify the stakeholders of the innovation ecosystem, structure them by subsystem categories, sphere and level of influence, to model the interaction of stakeholders within the innovation ecosystem. Understanding the systemic roles and interactions of stakeholders is critical to gaining a more accurate and detailed view of their contributions. A purposeful approach to building an innovative ecosystem allows you to form stakeholders to ensure their effective interaction.