In the market conditions of small and medium-sized enterprises development, the choice of a strategic direction is primarily connected with the desire to reduce production risks in the enterprise. When organizing production activities, a small and medium-sized business enterprise gives preference to those branches of agriculture, that do not require large investments, provide high economic efficiency, and whose products are in demand in the market. The article deals with the application of economic and mathematical methods for selecting a rational organizational and production structure of a small and medium-sized business enterprise, taking into account the production potential and production efficiency. The economic formulation of the task of justifying the rational organizational and production structure of an enterprise in a market economy should be formulated in accordance with the increase in the level of food provision for the population and focusing on making profit as a result of economic activity. Criteria for optimizing such tasks should be chosen: maximum profit or minimum arable land to provide feed for livestock sectors. The task is solved for the near future on the basis of the planned, regulatory and reporting information of a particular enterprise. We have developed the economic and mathematical model for optimizing the production parameters of the enterprise LLC “Surnay” of Baltasinsky district, which is typical for small and medium-sized businesses in terms of the composition of industries and the size of farmland in the Republic of Tatarstan. The economic and mathematical model of the posed task represents a logical system of the main branch and inter-branch relations in the production process. As a result of economic and mathematical modeling, a decision has been obtained that reflects the optimal content of the branches of a particular agricultural enterprise and contributes, in our opinion, to the effective use of productive resources (land, labor, etc.), which allows producing the maximum volume of output.