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Ensuring the rational use of limited space is a key function of government bodies at any level of power. Spatial development of the economy is modeled in the presented paper based on the concept of economic complexity. In addition to the innovative application of the economic complexity concept to the analysis of territorial systems in the form of macroregions, this study used an improved methodology for calculating the index of economic complexity in relation to the processes of interregional cooperation. The methodology of constructing a model of the spatial organization of the economy included determining the composition of the system of equations and their structure, formulating the prerequisites and limitations of the model, and determining an objective function of the model. The minimum level of heterogeneity of spatial development and the maximum of macroregion economic complexity indexes were chosen as the criterion of optimality. As a result of testing the model on real statistical data of the regions in Russia, a grid of macroregions was formed, providing an increase in the diversification of the types of production activities within the macroregion and a decrease in the differentiation of the development of the territories included in it. A computer program was developed during the course of the study that allows simulation experiments to be carried out in order to find the optimal variant of spatial organization of the economy. In addition, in the example of the aerospace industry, the management algorithm of the regional sectoral branching process was tested.