The paper studies and summarizes some theoretical views on the essence and content of the management system of the agro-industrial complex in the Kyrgyz Republic: the problems, shortcomings, experience in the implementation of economic reforms and the possibility of its use in local conditions. The study features the state of socio-economic development of the republic in the current market conditions. The research on the interaction of management bodies allows the authors to reveal some tendencies of development of the agro industrial complex. The paper introduces a mechanism for improving the interaction of the management system, practical approaches to economic programming and solving management problems in agro-industrial complex and economic policy. The proposals developed for the organization of corporate management of the agro-industrial complex will contribute to the successful solution of various tasks: to increase the economic efficiency of the agricultural sector, to raise the competitiveness of agricultural products and, ultimately, to provide the food security of the Kyrgyz Republic. The paper features a methodology for the rational organization of corporate governance. The methodology takes into account the individual characteristics and parameters of enterprises of various institutional forms of economic environment, geographical location and many other macro and microeconomic factors, as well as the interests of the state and regional business.