A rationale for the set of theoretical and methodological techniques of mapping and deep modeling in the Russian Arctic shelf and adjacent sedimentary basins in continental Russia is based on the materials for the Barents and Kara Seas region. This article provides the factual basis of the research and shows how to apply zonal-block model of the crust and generalized models of geodynamic settings in terms of the different geophysical data inconsistency. The necessity and approach for global and regional paleo-reconstructions are also discussed. It is shown that localization of the principal structural and compositional units of the lithosphere being a consequence of geodynamic processes at the boundaries of lithospheric plates, form at the basis of sedimentary cover and crystalline basement layered maps as well as cross-sections of the continental crust. The identified parameters of the deep structure and milestones of the regional tectonic history open new opportunities to explore the regularities of ore deposits distribution. The shown example of the forecast and metallogeny problems solution within Western Siberia and Khatanga-Vilyui petroleum provinces is made using the parameters of known industrial oil and gas fields for training the pattern recognition system.