Methodological and methodical fundamentals of the complex objects proactive management theory based on the fundamental results obtained in the interdisciplinary field of system knowledge are proposed. The paper provides information on the developed innovative polymodal complexes, combined methods, algorithms and techniques to solve various classes of problems of operational structural and functional synthesis and management of the development of the regarded classes of complex objects. The paper gives examples of solving practical problems for such subject areas as spacecraft, logistics, industrial production.