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• The aeolian sand thickness governs the hydrothermal regime of the shallow soil. • The aeolian sand cover increases the amplitude of variation on soil temperature. • The aeolian sand cover decreases the soil water content. • The aeolian sand cover weakens the soil heat budgets. The hydrothermal process within the aeolian sand layer on the Qinghai-Tibetan Plateau (QTP) plays a key role in understanding the interaction between desertification and underlying frozen soil. However, little is known about the hydrothermal dynamics of aeolian sand and underling soil layer in the frozen soil zone on the QTP. In this study, a sparse vegetation cover site and three aeolian sand cover sites with different sand thicknesses were established to study the hydrothermal dynamics within aeolian sand layer. The results show that the thickness of aeolian sand is critical in the soil hydrothermal process under sand cover. The increase in thickness of the aeolian sand layer resulted in an advance in the onset of the freezing and thawing of soil, and accelerated movement of the freezing and thawing front. In addition, the increase in sand thickness caused an increase in soil temperature during the thawing stage and the warming period of the thawed stage, whereas a decrease occurred during the cooling period of the thawed stage, the freezing stage and the frozen stage, which ultimately caused the enlargement of the annual range of ground temperature. Furthermore, in the study area, the actual evapotranspiration of sand-covered surface was larger than that of the naked surface. The water content also decreased with increasing sand thickness in different stages, which separately decreased the heat budget in both the warm and cold season because of the smaller thermal conductivity of aeolian sand with a lower water content. This study states that through the special hydrothermal process, have an adverse impact on the occurrence and formation of the frozen soil in the QTP. [ABSTRACT FROM AUTHOR]