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Crushed rock embankments are widely applied in the Qinghai-Tibet Railway. Most of previous studies have focused on the short-term cooling performance of crushed rock embankments, but few studies have concerned about the long-term cooling effect to ensure its service performance though monitored data. The long-term cooling effects of the U-shaped crushed rock embankment (UCRE), closed-system crushed rock-based embankment (CCRBE) and open-system crushed rock-based embankment (OCRBE) were evaluated based on 13-year monitored data at the Beiluhe experimental section. Compared with the conventional roadbed, the average ground temperature in 2017 at depths of 2, 5, and 10 m with the UCRE was decreased by 2.20 degrees C, 1.60 degrees C, and 0.94 degrees C, respectively. In the OCRBE, the mean annual temperature at the same depths dropped by 1.67 degrees C, 1.26 degrees C, and 0.80 degrees C, respectively. The mean annual temperature with the CCRBE dropped by 1.20 degrees C, 0.79 degrees C, and 0.45 degrees C, respectively. Therefore, the UCRE has the best long-term effect to decrease the temperature of underlying permafrost. Otherwise, crushed rock embankments existed as a staged cooling process. Engineering activities decreased temperature of underlying permafrost in short-term, but climate warming had a negative impact on the long-term cooling effect