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The report is devoted to a problem of mathematical modeling of the Earth System, which includes such components, as the atmosphere, ocean, land, cryosphere (continental and sea ices, permafrost) and the biosphere. Dynamics of the Earth System is regulated by physical, chemical, biological and other processes that demands interdisciplinary approaches at its research. In the report the main attention is paid to three global aspects of this problem: the supercomputer numerical technologies based on modern methods of applied mathematics; the description of processes taking place in the system, explicitly at the scales resolved by model, and in the parametrized way – at subgrid scales; mathematical questions (methods of the theory of dynamic systems and the sensitivity problem). The results received with climatic model of the Institute for Numerical Mathematics of the Russian Academy of Sciences (INM RAS) within the international project of comparison of such models (reproduction of modern climate and an assessment of its possible changes in the future) and with an operational weather forecasting model of INM RAS/Russian Hydrometeorological Center (including, at a seasonal scale) are presented. Finally, perspectives of further development of models of the Earth System for investigation of fundamental problems of its dynamics and for practical applications are considered.