The article considers the current and future systems for assessing the effectiveness of the use of state resources to create a national innovation system as a factor in improving the economic security of the state, the author develops a methodological approach to assessing the effectiveness of the use of state resources to create a national innovation system. The cyclical development of the world economy in the conditions of globalization is connected, first of all, with the change of technological structures, as well as with the provision of competitiveness for all levels of economic management. In the domestic and foreign economic literature, there is an idea of the national innovation system, which covers all types of economic objects in the country with innovations, increasing their competitiveness, and, thus, the national economy as a whole, and also directly affects the increase in the level of economic security of the country. Most developed countries and many developing countries have already established or are in the process of establishing their national innovation systems, built either on the basis of models already known and tested in other countries, or new, unique models for building innovation systems. The differences between these models of creation of national innovation systems of different countries are, both in the levels of economic objects, which are the basis of innovative breakthrough, and in the degree of use of public resources: "centralized model", based on public resources, or "market model", or a mixed model of "public-private partnership". These issues are the basis for consideration of the presented article. The methodological basis for writing the article was modern scientific research methods, including: dialectical method, method of system analysis, methods of analogy, comparative analysis, expert methods, structural-functional and normative approaches.