The main aim of this research was to search for relevant indicators and effective instruments for modeling the impact and institutional management of the regional innovation system for its balanced development. The objective of the study was to justify approaches for institutional management elaboration for balanced sustainable development of regional innovation systems regarding related factors and the needs of the region. The methodology of cognitive modeling and scenario impulse modeling are used for the analysis of the interconnection between the regional innovation system and higher education institutions and developing an instrument to diagnose the problems of no-congruence and improving the institutional management elaboration in the regional innovation policy. The analysis of system indicators of the cognitive map allowed to define the basic patterns in the regional system, determine the most significant factors and relationships for the economic system of the region and visualize them in the form of a cognitive map, identify the influence of the innovation environment elements on the target indicators, quantify its positive and negative impact, forecast and determine the directions of its improvement and enhancing the interaction of regional actors. The results of the study have practical value for use in improving institutional management in planning reforms and transformations of regional innovation systems.