Climate warming can enhance the decomposition of soil organic matter (SOM), thereby increasing the rate of carbon release from soils. In permafrost regions, climate warming alters the nature of freeze–thaw cycles by affecting sub-surface hydrology and soil temperature, thereby impacting the decomposition of SOM. However, this process is rarely considered in projections of the long-term dynamics of soil organic carbon (SOC) on the Tibetan Plateau (TP) in response to climate change. Here, we employ the CENTURY-FTC model, which implements a freeze–thaw module in the CENTURY model, to simulate the response of top soil organic carbon density (SOCD) at 0–20 cm depth to climate change in the permafrost region of Northern Tibet. Our findings suggest that (i) the average SOCD was 2.123 kg C m⁻² in 2015; (ii) the SOCD decreased at an average rate of 0.7 × 10⁻³ kg C m⁻² year⁻¹ for the period 1961–2015; and (iii) SOCD decreases spatially from south to north across Northern Tibet. Under various climate scenarios, the SOCD is projected to decrease significantly throughout Northern Tibet from 2016 to 2050, with the decline being most pronounced under the representative concentration-pathway (RCP) 8.5 scenario, which projects an increase in global mean surface temperature of 4.5 °C by 2100. Superimposed on this pattern, regional differences might be driven by vegetation type, with the largest decrements occurring in southern, alpine-meadow-dominated areas and the smallest in the northern alpine desert. We propose that this declining trend will be enhanced as climate warming continues and might be amplified by the increase in freeze–thaw processes. The addition of a freeze–thaw module to the CENTURY model changes projections of SOCD change due to climate. Whereas the freeze–thaw cycle has had little impact during the baseline period, its influence is likely to increase as climate warming continues. By 2050, freeze–thaw processes are projected to contribute 3% to SOCD decline under the RCP2.6 scenario, which projects a rise in global mean surface temperature of 1.5 °C by 2100, and as much as 10% under the RCP8.5 scenario. In general, future warming is likely to result in declining SOCD throughout Northern Tibet and a reduction in the capacity of alpine soils to sequester carbon.