The article is devoted to the current topic of choosing the optimal organizational option of multilateral integration of the scientific and educational sphere, business and the state in the process of globalization of the world economy. The authors justify the format of formation of scientific and educational complex on the basis of network interaction, which allows to obtain the greatest synergistic effect. In order to justify the effective network interaction of the scientific and educational complex, an analysis of existing methods of assessing the efficiency of its functioning was carried out and an author’s system of performance indicators and its assessment was proposed in accordance with the general purpose of the integration mechanism and the specific purpose of each interaction subject. The model contains a system of heterogeneous indicators reflecting the principles of formation of a scientific and educational complex on the basis of network interaction, which allows, along with an evaluation task, to determine, using factor models, further directions of inter-network relations of subjects in order to better understand the current processes and identify problem areas of coordination of their innovative activity.