Aeolian sand significantly affects permafrost degradation, but the effect of the aeolian sand on the permafrost on the Qinghai-Tibet Plateau remains unknown. The sand layer thickness is critical to its role. However, little quantitative research has been conducted on the effect of the sand layer thickness on its role. In this study, using CoupModel, we investigated the differences in the impact of the aeolian sand cover on the hydrothermal state of permafrost with 20 different sand layer thicknesses (10 ∼ 200 cm, 10 cm increment) and analyzed the mechanisms that explain the different impacts. The results reveal that the active layer is where the aeolian sand has the most impact on the permafrost. The aeolian sand layer accumulates precipitation into the soil below the sand, thereby significantly drying the shallow soil layer of the current stratum. Moreover, the thicker the sand layer, the more water accumulates in the underlying soil layer. In the middle-upper active layer, the initial soil heat storage, soil heat flow interception, and liquid water and ice contents govern the soil temperatures that increase in cold seasons and decrease in warm seasons as the sand layer thickens. Near the bottom of the active layer, the initial soil heat storage and soil heat flow interception control the soil temperatures that increase in cold seasons but fluctuate between sand layer thicknesses of 50 cm, 70 cm, and 120 cm in warm seasons as the sand layer thickens. Permafrost degradation is enhanced by sand layers thinner than 150 cm and retarded by sand layers thicker than 150 cm, respectively. The thermal state, soil properties, and accumulation process of the aeolian sand also contribute to this effect of the aeolian sand on the permafrost. In the plateau aeolian deserts, the sparse vegetation promotes permafrost degradation and the thinner seasonal snow cover protects permafrost. Moreover, under the different climate during the geological history period, the island or discontinuous permafrost might be formed due to the pluvial-radiation talik caused by the thicker sand layer or dunes.