The relevance of the researched problem is caused by the increasing interest in using potential of transdisciplinary approaches, and mathematical methods, which include the game theory in analysis of public and economic processes. The aim of the article is studying a possibility of implementation of the transdisciplinary approaches in economic researches. The leading approach is institutional and evolutionary, which allows to reveal such tendencies of relationship development and interrelations of individuals that remain hidden and implicit. It also allows to receive new and quite unexpected important results, significant for practice. In the article the hypothesis is proved. According to it, innovations, its generation and autopoiesis itself are structural units. In the innovative environment it assumes various forms. The materials of the article can be useful for development of the theory of the system analysis, and also when developing macroeconomic forecasts of social and economic development.