Effective management of the agricultural economy requires the development of new methodological approaches, taking into account the formation of the digital economy sector. In this paper, the economic schools that describe organizational and economic mechanisms are analyzed and grouped. At all schools, Russian economics is characterized by the division of the organizational and economic mechanism into two subsystems: the subject of management and the object. The real sector of the economy finds itself in the position of an object of influence. The hierarchical approach is used to form the mechanism of digital transformation of the agro-industrial complex in the Russian Federation. The purpose of the mechanism is the development of advanced technologies in accordance with federal programs. The disadvantage of this approach is the lack of feedback. For some types of farms, the transaction costs of following these programs are higher than the benefits of their implementation. Western economic schools, on the contrary, consider a business (firm) to be a subject of the economic mechanism. The methods of regulation (laws, norms, etc.) are secondary to the interaction of subjects. According to some authors, the digital economy is a radically new mechanism of influence that will overcome the contradictions between the hierarchical management mechanism and the self–regulation of systems. But in most works, digital transformation is seen as a company's transition to new technologies. At other levels, the process should be based on the global dissemination of information technology. The disadvantage of this approach is the inability to correct «market failures» and stimulate the development of digital technologies in problematic industries. The neo-endogenous approach unites the positions of the Russian and Western schools. In this paradigm, it is supposed to optimize the development of rural areas on the basis of local initiatives, «smart» technologies, regulatory impact and subsidies from the center (region, country, UES).