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It has been proven that crushed rock layers used in roadbed construction in permafrost regions have a cooling effect. The main reason is the existence of large porosity of the rock layers. However, due to the strong winds, cold and high radiation conditions on the Qinghai-Tibet Plateau (QTP), both wind-blown sand and/or weathered rock debris blockage might reduce the porosity of the rock layers, resulting in weakening the cooling effect of the crushed rock layer (CRL) in the crushed rock embankment (CRE) of the Qinghai-Tibet Railway (QTR) in the permafrost regions. Such a process might warm the underlying permafrost, and further lead to potential threat to the QTR’s integrity and stability. The different porosities corresponding to the different equivalent rock diameters were measured in the laboratory using water saturation method, and an empirical exponential equation between porosity and equivalent rock diameter was proposed based on the measured experimental data and an important finding is observed in our and other experiments that the larger size crushed rock tends to lead to the larger porosity when arbitrarily packing. Numerical tests were carried out to study impacts of porosity on permafrost degradation and differential thaw depths between the sunny and shady shoulders. The results show that the decrease in porosity due to wind-blown sand or weathered rock debris clogging can worsen the permafrost degradation and lead to the asymmetric thermal regime. In the traditional embankment (without the CRL within it), the largest differential thaw depth can reach up to 3.1 m. The optimized porosity appears in a range from 34% to 42% corresponding to equivalent rock diameter from 10 to 20.5 cm. The CRE with the optimized porosities can make underlying permafrost stable and 0℃ isotherms symmetric in the coming 50 years, even under the condition that the climate warming can lead to permafrost degradation under the CRE and the traditional embankment. Some practical implications were proposed to benefit the future design, construction and maintenance of CRE in permafrost regions.