The crushed-rock interlayer embankment with ventilation ducts has been advocated to stabilize the permafrost stratum under expressways in permafrost regions. This embankment must render better cooling effect than railway embankments because the expressway surface is wider and hotter. To this purpose, the walls of the ventilation ducts need to be perforated. This study evaluates the cooling performance of the rushed-rock interlayer embankments with unperforated and perforated ventilation ducts along an expressway in permafrost regions of the Qinghai-Tibet Plateau. A three-dimensional numerical model is developed based on heat and mass transfer theories. The model includes the coupled heat transfer between air and ventilation duct wall, the air convective heat transfer in crushed-rock layer, and the heat conduction with phase change in soil layers. The numerical results indicate that if the ventilation ducts are perforated and embedded at the top of the crushed-rock interlayer, the cooling effect of the embankment can be greatly enhanced. A good cooling performance can still be achieved even if the centerline spacing of the perforated ventilation ducts is enlarged to 4 m to facilitate the construction. The crushed-rock interlayer embankment with perforated ventilation ducts is a better candidate structure for expressways in permafrost regions of the Qinghai-Tibet Plateau.