The review addresses physico-chemical aspects of interaction between macro-, micro-and nano-structured units of matter with the analysis of interface and grain boundary entities (nonautonomous phases) mechanisms and formation, as well as methods of their control in order to achieve the desired functional properties of nanostructured materials. Construction of these materials involves identification of thermodynamic and kinetic regularities in the organization processes, state and genesis parameters of nonautonomous phases formed as specific nanosized structures in a limited space between the macroscopic volume phases and with the limited amount of substance, which differ significantly on their properties, structure and composition from the appropriate characteristics of volume phases. Studying them is based on the application and development of theoretical and experimental methods of non-equilibrium thermodynamics, chemical kinetics, nonlinear dynamics and fractal analysis to determine the conditions of self-organization or materials directed synthesis with a high content of nonautonomous phases.