Aeolian sand has damaged the Qinghai-Tibet Railway. In this study, the impact of aeolian sand on cooling effect of crushed-rock embankment of Qinghai-Tibet Railway is investigated on the basis of a coupled mathematical model of convective heat transfer and heat conduction with phase change. In addition, climate warming is also considered. The results show that extensive convection can be produced in the layer of block-stone for open block-stone embankment. After the crushed-rock layer filled with aeolian sand, it is clear that the cooling effect of crushed-rock embankment will drop off, which can be seen by analyzing velocity variation in the rock layer, then permafrost table will rise gradually. The cooling mechanisms of the closed embankment significantly depend on natural convection. The artificial permafrost table beneath the center of embankment is higher than that of the adjacent regions due to the impact of filling soil. After the surface of closed rock layer buried by aeolian sand, natural convection intensity weakens gradually. In addition, the cooling effect of rock layer can counteract the negative effect of climate warming and can uplift the permafrost table. The results can provide a guide for the infrastructure design and reinforcing Qinghai-Tibet Railway in permafrost regions.