A conceptual model of the organization and functioning of the agro-industrial complex management system as a mega-cluster formation has been constructed, which includes four main blocks: organizational, economic, legal and institutional, which contain their inherent instruments and levers of regulation. Based on the above, the definition of the management model of the agro-industrial complex as a mega-cluster organization has been formulated. In development, an appropriate definition of the organizational and economic model of corporate governance of the agro-industrial complex as a mega-cluster is given. A set of factors that affect the management system in the agro-industrial complex has been established, and their brief interpretation is given. It has been established that in the modern practice of the agro-industrial complex, several main groups of models can be distinguished, typical for all levels of management: A. Incomplete – not all levels of management are covered; B. Traditional – all functions and organizational structures can be present in the management system; C. Market models – correspond to the specifics of management in market conditions; D. Innovative – based on combining the best aspects of all known models. On this basis, it was revealed that at present, the solution of most of the problems of the agro-industrial complex is possible, first of all, through the development of an end-to-end system of corporate management of agro-industrial production as a megacluster infrastructure.