The purpose of this study is to develop a methodology for assessing the level of economic security of innovative enterprises based on the use of taxonomic analysis of the main indicators of their institutional support for the optimal organization of management and forecasting the economic development of the regions of their operation. The method proposed in the article consists in assessing the system of indicators of institutional support for innovative entrepreneurship within the framework of the Institute of Human Capital, the Institute of Financial and Credit Component, the Institute for the Implementation of Innovations in Industry, the Institute of Export Activities, the Institute of Intellectual Property, the Institute of Infrastructure Support, the Institute of Regulatory and Legal Support, the Institute of Public-Private Partnership and Mediation, the Institute of Information Support. The advantage of this technique over the methods for assessing economic security proposed in other scientific works is that the summary assessment indicator is universal and its interpretation makes it possible to identify the relationship between the main integrated indicators for all regions of the studied country, taking into account the unevenness of their economic development, as well as to analyze the question of the causal nature of the transformation of the institutional environment and its consequent. The practical significance of systematized indicators of institutional support, influencing the modeling of economic security management of innovative entrepreneurship, is that they can be used in forecasting the economic development of regions of the country and developing appropriate measures to regulate this process.