Crushed rock materials had been utilized extensively upon embankments, termed as crushed rock embankment (CRE), along the Qinghai-Tibet Railway in permafrost regions. Based on a long-term monitoring system along the railway, thermal stability and deformation characteristics and mechanisms of CRE were analyzed by field monitoring datasets from 2005 to 2009. The thermal stability analyses indicated that permafrost tables beneath CRE all had upwards movements but to varying degrees. For U-shaped crushed rock embankment (UCRE), the thermal stability of underlying permafrost kept well; along with permafrost table moving upwards, the shallow ground temperatures beneath the embankment decreased obviously while deep ground temperatures kept almost constant. For crushed rock revetment embankment (CCRE), the cooling effect was effective in cold permafrost regions. But in warm permafrost regions, the shallow permafrost beneath the embankment had no obvious cooling trend while the deep permafrost had a slight warming trend. The deformation analyses indicated that CREs experienced frost heave in permafrost regions with mean annual ground temperature (MAGT) < -1.5 °C but settlement in permafrost regions with mean annual ground temperature > -1.5 °C. The magnitudes of both heave and settlement were not significant. Since the better thermal stability of underlying permafrost, it was inferred that the settlement of CRE mainly originated from compression of warm and ice-rich permafrost layer near permafrost table.