The aim of the study is to form a control subsystem model in the management system of the region’s mineral resource complex. The article is devoted to solving the main task to form a flow diagram for operating the control subsystem in the management system of the region’s mineral resource complex for monitoring indicators of subprogram 1 “Reproduction of the mineral resource base, geological study of the subsoil” within the framework of the Russian Federation state programme “Reproduction and use of natural resources”. The concepts of the set-theoretic approach and the method of mathematical analysis are used in the paper. The work features are forming an algorithm for operating the control subsystem in the management system of the region’s mineral resource complex, using mathematical tools. As a result of the study, the proposed model of the control subsystem in the management system of the region’s mineral resource complex is tested on the example of statistical data on reserves for five types of solid minerals. The adequacy of the obtained model of the control subsystem in the management system of the region’s mineral resource complex is confirmed by the calculations carried out in the work. The simulated control subsystem can be replicated for other types of minerals.