The permafrost organic carbon (OC) stock is of global significance because of its large pool size and the potential positive feedback to climate warming. However, due to the lack of systematic field observations and appropriate upscaling methodologies, substantial uncertainties exist in the permafrost OC budget, which limits our understanding of the fate of frozen carbon in a warming world. In particular, the lack of comprehensive estimates of OC stocks across alpine permafrost means that current knowledge on this issue remains incomplete. Here, we evaluated the pool size and spatial variations of permafrost OC stock to 3 m depth on the Tibetan Plateau by combining systematic measurements from a substantial number of pedons (i.e. 342 three-metre-deep cores and 177 50-cm-deep pits) with a machine learning technique (i.e. support vector machine, SVM). We also quantified uncertainties in permafrost carbon budget by conducting Monte Carlo simulations. Our results revealed that the combination of systematic measurements with the SVM model allowed spatially explicit estimates to be made. The OC density (OC amount per unit area, OCD) exhibited a decreasing trend from the south-eastern to the north-western plateau, with the exception that OCD in the swamp meadow was substantially higher than that in surrounding regions. Our results also demonstrated that Tibetan permafrost stored a large amount of OC in the top 3 m, with the median OC pool size being 15.31 Pg C (interquartile range: 13.03–17.77 Pg C). 44% of OC occurred in deep layers (i.e. 100–300 cm), close to the proportion observed across the northern circumpolar permafrost region. The large carbon pool size together with significant permafrost thawing suggests a risk of carbon emissions and positive climate feedback across the Tibetan alpine permafrost region.