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Permafrost warming and potential soil carbon (SOC) release after thawing may amplify climate change, yet model estimates of present-day and future permafrost extent vary widely, partly due to uncertainties in simulated soil temperature. Here, we derive thermal diffusivity, a key parameter in the soil thermal regime, from depth-specific measurements of monthly soil temperature at about 200 sites in the high latitude regions. We find that, among the tested soil properties including SOC, soil texture, bulk density, and soil moisture, SOC is the dominant factor controlling the variability of diffusivity among sites. Analysis of the CMIP5 model outputs reveals that the parameterization of thermal diffusivity drives the differences in simulated present-day permafrost extent among these models. The strong SOC-thermics coupling is crucial for projecting future permafrost dynamics, since the response of soil temperature and permafrost area to a rising air temperature would be impacted by potential changes in SOC.