Tibetan permafrost largely formed during the late Pleistocene glacial period and shrank in the Holocene Thermal Maximum period. Quantifying the impacts of paleoclimatic extremes on soil carbon stock can shed light on the vulnerability of permafrost carbon in the future. Here, we synthesize data from 1114 sites across the Tibetan permafrost region to report that paleoclimate is more important than modern climate in shaping current permafrost carbon distribution, and its importance increases with soil depth, mainly through forming the soil's physiochemical properties. We derive a new estimate of modern soil carbon stock to 3 m depth by including the paleoclimate effects, and find that the stock ([Formula: see text] PgC) is triple that predicted by ecosystem models (11.5 ± 4.2 s.e.m PgC), which use pre-industrial climate to initialize the soil carbon pool. The discrepancy highlights the urgent need to incorporate paleoclimate information into model initialization for simulating permafrost soil carbon stocks.