Chemical composition of soil organic matter determines its decomposability and may affect soil microbial activity. This is very important for understanding variability in soil organic carbon pools in context of changes in plant cover or climate. This paper is aimed to characterize existing carbon pools and molecular organization of the humic acids, isolated from various permafrost-affected soils of Yamal region and to assess the potential vulnerability of soils organic matter in context of possible mineralization processes. Soils for most of studied sites were characterized predominantly by acidic to strong acidic pH. Profile distribution of carbon, nitrogen and C:N ratio showed non-gradual changing with the depth due to manifestation of cryopedogenesis in soil profiles which lead to cryogenic mass transfer. Mean soil organic carbon stocks for the study area were 7.9 ± 2.2 kg m⁻² (for 0–10 cm layer), 15.0 ± 5.5 kg m⁻² (for 0–30 cm), 24.0 ± 8.0 kg m⁻² (for 0–100 cm). Analysis of soil organic carbon stocks among predominant soil types (Russian soil classification system) revealed relatively high variability of values in 0–10 cm (from 4.5 kg m⁻² in Peaty Gleyzem underlain by permafrost to 9.6 kg m⁻² in Peaty Podzol underlain by permafrost) and 0–30 cm layers (from 9.9 kg m-2 in Cryic Podbur underlain by permafrost to 24.1 kg m⁻² in eutrophic peat soil underlain by permafrost). Results of solid-state ¹³C NMR spectrometry showed low amounts of aromatic fragments in studied soils. All studied soils are characterized by predominance of aliphatic structures, and also carbohydrates, polysaccharides, ethers and amino acids. High content of aliphatic fragments in studied humic acids shows their similarity fulvic acids. Low level of aromaticity reflects the accumulation in soil of poorly decomposed organic matter due to cold temperatures. Our results provide further evidence of high vulnerability and sensitivity of permafrost-affected soils organic matter to Arctic warming. Consequently, these soils may play a crucial role in global carbon balance under effects of climate warming.