Dissolved organic carbon (DOC) export from arctic rivers is a critical component of the Arctic carbon cycle. Investigating the influence of environmental factors on DOC concentration dynamics is crucial for understanding the implications of climate warming. However, permafrost is often overlooked in quantitative analyses of DOC concentration variations. Therefore, it is critical to investigate the relationship between permafrost and DOC in the Arctic. Permafrost degradation alters the hydrological pathways of Arctic rivers and releases large amounts of stored organic carbon, which significantly impacts the terrestrial-aquatic carbon flux and global biogeochemical cycles. Understanding the seasonal dynamics of permafrost thaw depth and its impact on DOC export is essential for improving biogeochemical models and predicting carbon flux changes under future climate warming scenarios. The study focuses on the six major arctic river basins within permafrost regions, calculating riverine DOC concentrations and permafrost thaw depths from 2003 to 2020. The DOCUVFW method was employed in conjunction with remote sensing data to calculate DOC concentrations at river mouths from 2003 to 2020. Permafrost thaw depth data were estimated using the Stefan solution within the basins. A generalized additive model (GAM) was used to evaluate the contributions of permafrost thaw depth to estuary DOC concentrations and to further analyze how permafrost soil characteristics influence the DOC migration process. The results showed that: (1) From 2003 to 2020, the DOC concentration in the Arctic region, transported by rivers from land to the ocean, increased from 76.7 μmol/L to 101.3 μmol/L, showing a significant upward trend. (2) The influence of permafrost thaw depth on DOC concentration remained gradual during the initial thaw period, followed by a marked increase during the rapid thaw period, with contribution rates ranging from 22.2% to 77.1%. In the complete thaw phase, the impact slightly decreased. (3) Using K-means clustering, arctic river basin soils were classified into four groups. Soils with high drainage capacity resulted in a rapid response of river mouth DOC to thaw depth, while soils with low drainage capacity facilitated the conversion of soil organic carbon to DOC. Soils with strong DOC adsorption capacity reduced DOC output in the later stages of thaw, while soils with weak adsorption capacity promoted a continuous increase in river mouth DOC concentration. This study highlights the significant role of permafrost thaw depth and soil properties in regulating DOC dynamics in arctic river basins. The results also suggest that soil characteristics, such as drainage capacity and DOC adsorption ability, play a crucial role in controlling DOC export and its seasonal variations in the Arctic region.