The article presents the science, technologies and innovations as foundations of modern economic development. The purpose of establishing complex-structured innovation enterprises and their functions are analyzed. An effective organizational-economic structural model is proposed for the management of their performance. Hierarchic models are developed corresponding to the problems posed to each structure. a conceptual algorithm is developed for of finding an agreed solution on product/service output among models with various levels based on the efficient utilization of scarce resources (pp.61-70).