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One of the most prominent problems of modern geochemistry and climatology is the understanding of the patterns of migration of the main greenhouse gases, carbon dioxide (CO₂) and methane (CH₄). The purpose of this work is a brief review of the widely accepted concept of the dominant role of the anthropogenic factor in climate change, which is considered in the paleo-context of changes in natural climate cycling over the past hundreds of thousands of years, and in present time. It is shown that to understand the functioning of the climate system, it is necessary to take into account the geological factor – changes in the state of terrestrial and subsea permafrost: the huge reservoirs of ancient carbon, which is included in biogeochemical cycles due to permafrost degradation in warm geological epochs. This leads to imbalance in the carbon cycling, which manifests itself in massive emissions of CO₂ and CH₄ into the atmosphere. During cold geological epochs, carbon accumulates in permafrost, which stores amounts of carbon exceeding the carbon exchange between atmosphere, biosphere, land and ocean. Considering the Arctic region as the key climate “kitchen” we state that present time is characterized by unique long-lasting warming after the Holocene optimum, which occurred in the northern hemisphere approximately 5–6 thousand years ago. It contradicts with the Milankovich’ 105-kyrs cycling: after the Holocene optimum, the geological ice-epoch should have occurred, which should have led to about 100-meters sea level lowering and the transformation of the shallow Arctic shelf into land. However, warming has continued and the level of the World Ocean continues to rise, which has already led to an extended high sea level on the Arctic shelf – unique in geological history. This caused the lasting contact of relatively warm bottom waters (~(–1) °C) and frozen sediments (~(–25) °C) of the Arctic shelf for 5–6 thousand years longer than in previous warm geological epochs, which led to the progressive degradation of subsea permafrost, formation of deep or through taliks (zones of melted permafrost) and destabilization of Arctic shallow hydrates. It is shown that the increasing runoff of Siberian rivers, mobilization, transport, and transformation of terrestrial organic matter in the Arctic land–shelf system determines the sedimentation and biogeochemistry of the East Siberian Arctic Shelf – the broadest and shallowest shelf in the World Ocean, which makes up more than 70% of the Northern Sea Route area. This review paper presents selected key results obtained by the authors and their colleagues over the past 30 years, and identifies a number of problems facing modern climatology.