Ventilation embankments, including those with forced ventilation, natural ventilation, and combination of these, were adopted for the construction of the Gonghe−Yushu Expressway in warm permafrost areas. To evaluate the actual thermal performance of ventilation embankment in the Qinghai−Tibet Plateau, four types of ventilation embankments were selected as objects, and their long-term thermal characteristics were analyzed based on monitoring data. It was found that: 1) under the strong scale effect of a wide embankment, the crushed-rock embankment (CRE) was warming up and the permafrost table was declining year by year. Meanwhile, the combined ventilated slab and CRE and ventilated ducts embankment can effectively decrease the ground temperature and raise permafrost table in the year with a colder winter; 2) transverse temperature difference caused by the shady–sunny slope effect existed in all the four embankments. However, it was weakened by the combined ventilated slab and CRE and the ventilated ducts embankment due to their stronger cooling effect; and 3) the pre-existing embankment had a remarkable thermal disturbance to the adjacent newly-built embankment, so a reasonable embankment spacing should be considered in practical engineering. These findings would provide a reference for construction of expressway embankments in permafrost regions.