The development of the regional innovation ecosystem influences the level of development of innovative activity in the region and in the country as a whole. We have refined the concept of the innovation ecosystem and, based on this concept, determined that it reflects the level of development and the performance of regional innovation ecosystems. We have devised a system of indicators for assessing the performance of innovation ecosystems, consisting of indicators for assessing the level of development and the performance of innovation ecosystems. The direction reflecting the level of development of innovation ecosystems is composed of indicators of the presence of subjects of innovative activity and indicators of innovative activity. The direction reflecting the performance of innovation ecosystems includes indicators of the emergence of an innovative product or service and indicators of the commercialization of the innovative product or service. Additionally, we have given our own explanation of the integration of the regional innovation ecosystem into the national one and identified the indicators of integration. The selected integration indicators include the amount of regional normative acts in the sphere of innovative development, the indicators of involvement of regional budgetary funds in innovative development, as well as the indicators of formation of the innovative infrastructure at the regional level. The proposed methods of assessing the performance of regional innovation ecosystems and the degree of their integration into the national innovation ecosystem help identify the existing degree of involvement in creating a supportive environment for innovative development of the federal subject, in addition to providing the conditions at the national level; to determine the cause and effect relationships of integration processes and indicators of development of national and regional innovation ecosystems; to identify the factors influencing the growing number of participants in the innovation ecosystem and the connections created between them, to determine their development; to identify the opportunities for analysis of volume, types and directions of resource movement between the agents of the innovation process, as well as to develop suitable tools for globalization of the regional innovation ecosystem in the future, namely, the development of cluster systems and diversification of external relations, maintaining and strengthening the global position.