Considering the climate warming, the block stone embankment and the ventilation duct-closed block stone embankment are becoming the major structures of cooling embankments in permafrost regions. In order to obtain the seepage characteristics and the properties of block stone layers with different sizes, wind tunnel tests were carried out in this study. On the one hand, the statistical relationships between the permeability/inertial resistance coefficient and the cement ball's diameter were gotten. On the other hand, the nonlinear quadratic curve relationship between the internal air pressure gradient and the seepage velocity within the cement ball layer were acquired. In addition, based on the parameters and relationships from the wind tunnel test, coupled heat transfer model in porous media was used to analyze the cooling effect of the close block stone embankment in the Chai-Mu Railway using finite volume method, and the reliability of the numerical model and parameters were verified by the observed values. Furthermore, the long cooling effects of the closed block stone embankment, the block stone interlayer embankment and the ventilation duct-closed block stone embankment in the Qinghai-Tibet High-Grade Road were analyzed through the closed block stone embankment model. It is found that the closed block stone embankment and the ventilation duct-closed block stone embankment could cool down the permafrost effectively, raise the artificial permafrost table and insure the artificial permafrost table higher than the original one in the background of climate warming in the study period. The block stone interlayer embankment could raise the artificial permafrost table in a short period of time, but the temperature of permafrost under the embankment would be elevated.