Permafrost soils contain vast carbon stores that release greenhouse gases when thawed, but current climate projections rely on oversimplified two-layer models distinguishing only the seasonally thawing "active layer" from underlying frozen "permafrost." This approach neglects the complex thermal history and vertical structure of Arctic soils, particularly a critical "transition zone" that alternately freezes and thaws over decadal to centennial timescales in response to climate variations and contains high concentrations of ground ice and organic matter3. Here we show that change point detection on high-resolution radiocarbon measurements of bulk soil reveals three distinct layers—active, transient, and intermediate—that record thaw history and carbon dynamics within the upper two meters of the landscape. As components of the transition zone, the transient layer marks the maximum modern active layer to which the upper soil thaws each summer, while the intermediate layer stores millennial-aged carbon from Holocene warm periods. Today, gradual thaw as well as disturbances such as wildfires are causing ground-ice melt and transition zone collapse, exposing much older permafrost carbon to the atmosphere. Therefore, expanding depth-resolved datasets is essential for recognizing the full vertical structure of the soil-permafrost complex and strengthening projections of Arctic landscape stability and carbon release.