Topicality. In the economy of Ukraine, there are macroeconomic, inter- and intra-sectoral, regional disparities, the appearance of which is due to the existing structure of the economy, the focus on raw material exports, low-tech production, uneven inter-sectoral development, the discrepancy between the needs of the regions and their returns, and many other reasons. The presence of these disparities not only slows down the development of the economy, but also threatens the economic security of Ukraine.Aim and tasks. Taking into account the specified strategic directions, the following tasks are set in the work: to determine the factors influencing the economy and its sectors, which lead to the emergence of structural disparities, to determine the peculiarities inherent in the agro-industrial sector, to identify and systematize the influencing factors in order to develop a strategy and management system based on resilience, to develop methodological approaches to identifying structural disparities in the agri-food sector of the economy.Materials and Methods. Identification of structural disparities, assessment of their effect and depth was carried out using methods of analysis and synthesis, scientific abstraction and statistical grouping, which made it possible to analyze the nature of the process of formation of disparities, to determine the most persistent violations of proportionality at all levels of development of the agro-food sector with the aim of targeted application of preventive prevention measures their negative impact and constructive way out of crisis situations.Research results. From the point of view of the axiomatic of the theory of complex systems, the mechanism of the emergence of structural disparities has been clarified, as a response to a high level of complexity, a rapid change in influencing factors that determine the dynamics of the development of the agro-food sector of the economy, and numerical risks caused by uncertainty, which provokes the emergence of conflict between individual subsystems of the agricultural sector. Priority zones of disproportionality were determined by studying the structure of the population according to individual characteristics.Conclusion. Ensuring sustainable development of the country and its economic security is achieved by the ability to resist the action of external and internal factors, existing and newly created at any economic level of disparities. The peculiarities of the strategy for the development of economic sectors on the basis of resilience are determined. It is shown that the implementation of such a strategy, for any sector of the economy, is based on a well-founded objective and the conclusions of the analysis of modern challenges and the intersection of the interests of market players.