Due to the increasing role of hydrocarbon resources in the development of the Russian economic system, as well as taking into account the need to study the economic processes taking place in modern enterprises of the fuel and energy complex, the problem of modeling their activities, with the involvement of the mathematical apparatus of matrix planning, becomes now while an even more significant. Formulated in the article the concept of modeling the economy of modern enterprises of the complex, involving the mathematical apparatus of matrix planning. An algorithm for synthesis of economic-mathematical model of the complex's companies in the market conditions based on the matrix-differential equations. Defined by the differential equations of the matrix planning in the development of modern economy the complex. The results of studies of the relationship of factors of production, demand and consumer criteria on the example of the complex companies. In the study, the authors concluded that the use of differential equations planning matrix allows one side of the energy companies to more accurately produce the strategy and tactics of its development, and on the other - to identify options for dynamic interactions Energy with related industries.