The local and world practice shows that clustering as a form of association of business entities for development of industrial and business activities is an important direction for development of agri-food sector, as well as the arrangement of territories based on efficient use of land, labor, material, technical and financial resources. The article dwells of studies of theoretical and methodological basis of megacluster development of agro-industrial complex. It has been determined that currently four possible concepts (paradigms) can be applied regarding agro-industrial complex (AIC): AIC as a self-sufficient system, AIC as a megacorporation, AIC as a specific market, AIC as a separate society. Study has been carried out and an integrated layout has been designed for arrangement and functioning of an integrated management system for agro-industrial complex sustainable development. Groups of factors determining stability of short-term and long-term development of agro-industrial complex as a megacluster are identified. A number of principles for sustainable functioning of agro-industrial complex as a megacluster were formed: Infrastructure balance, management system improvement, rational territorial and intrasectoral distribution of production, balanced agro-industrial production in terms of resources, etc. These principles and their interpretation have been formulated for agro-industrial complex as a megacluster for the first time. Their novelty consists both in aggregate selection, reflecting stable functioning of agro-industrial complex as a megacluster under new conditions, and in reflecting the most significant aspects of megacluster's activity being the main links in its sustainable functioning chain.