For the study of innovation processes taking place in our country, it is necessary choose the appropriate methodological approach. An adequate selection is possible only if there is enough understanding about the currently available concepts and theories, reflecting the patterns and characteristics of building innovation systems. Currently, within the individual areas of economic thought developed various theories of innovation. The article attempts to systematize the concepts, theories and approaches in the field of economic thought. As a main method of this study was used a systems analysis. As a methodological basis for the study of the innovation system is proposed to use the neo-institutional, systems and synergetic approach. Neo-institutional approach will allow include the micro-level research in the theory of the innovation system. A systems approach based on the principle of atomism, as well as holism allows to structure and to establish links between the elements and factors of development and to identify «bottlenecks» in the development of the innovation system. Synergetic approach provides an opportunity to take into account the dynamic aspect of development, such as the increase in the category of complexity, uncertainty, which is an inherent part of innovation.