The novel asphalt concrete waterproofing layer (ACWL) in high-speed railway faced a severe challenge from thermal fatigue cracking, while there was absence of a feasible evaluation method for this unique thermal fatigue mode. In this study, the overlay test (OT) was customized in terms of test temperature and open displacement to simulate the cyclic thermal load on in-service ACWL and characterize the thermal fatigue behaviors of railway asphalt mixtures. Four classical and two dissipated energy-derived indicators, namely maximum tensile load (L0), cracking rate index (CRI), the ratio of transitional tensile load L1 to L0 (L1/L0), pseudo fracture energy (PFE), initial dissipated energy (IDE), and cumulative dissipated energy (CDE), were utilized to evaluate the fatigue characteristics. It was found that the OT at a test temperature of 20 °C and open displacement of 0.6 mm was the most efficient in distinguishing fatigue characteristics, and the CRI, L1/L0, IDE, and PFE were statistically recognized to be feasible and effective. In addition, railway asphalt mixtures could achieve a 10-year fatigue life under moderate conditions while might crack rapidly at a low temperature and a large open displacement. Meanwhile, several indicators, including L0, CRI, L1/L0, PFE, and CDE, demonstrated linear relationships with the fatigue life on a normal or log scale at low temperatures, implying their potential to predict fatigue life. Finally, a Weibull damage model was applied based on load ratio-based damage degree, which had fair linear correlation with actual damage degree, to correlate with the thermal fatigue damage process. As expected, the proposed evaluation method, indicator, and fatigue damage model could fairly characterize the thermal fatigue behaviors of railway asphalt mixtures and further guide the construction and maintenance of ACWL.