Addressing the impact of climate warming and anthropic activities, crushed-rock layer (CRL) is a zero-carbon emission technology by using natural cold air to protect infrastructures in permafrost regions. But in cold sandy environment, the issue of its cold energy capacity on account of aeolian sand clogging needs to be solved. Based novel field experiments on Tibet Plateau, the dynamic evolution law and its controlling factors of natural cold energy accumulation of the CRL are quantitatively figured out. Results show that the initially open CRL had a strong forced convection of air in the first two winters, while the cooling effect was failure after the third winter. The filling of aeolian sand caused heat transfer mode of the CRL to change from forced convection to natural convection in cold season, losing the ability of “thermal semiconductor” aimed to mitigate permafrost degradation. The closed CRL represented weak natural convection in cold season and thermal insulation in warm season, which had better long-term cooling effectiveness than other conditions in the aeolian environment. As the thickness of the aeolian sand filling increased, the maximum Rayleigh number and natural convection time of the closed CRL decreased. Accumulation of cooling energy in cold season and thermal insulation in warm season were positive correlation with thickness of porous media layer. It was not recommended to solely adopt crushed rock embankment or crushed rock revetment in aeolian sand environment and regions with higher annual average temperature. The findings solved the scientific evaluation issue of cold energy storage capacity of CRL, and provided constructive engineering implications for its efficient application.