Taking the damping layer as the research object, first, by using the dynamic mechanical test, based on the high-order fractional derivative FVMP model, and in combination with the temperature-frequency equivalent principle, the temperature and frequency dependent properties of the damping layer was characterized. Then, the model was applied to the vehicle-CRTSIII slab ballastless track coupled system. Finally, the effect of the temperature and frequency dependent properties of the damping layer on track structure vibration response was analyzed. The results show that the temperature and the loading frequency have a significant impact on the dynamic mechanical properties on the damping layer and the high-order fractional derivative FVMP model can accurately characterize this property. In the time domain response, the peak values of the slab track displacement and the acceleration on the FVMP model are significantly larger than those on the K-V model. At each reference temperature point, the displacement response of the slab track on the FVMP model decreases with the decrease of temperature, while the acceleration of the slab track shows an opposite trend. In the middle and high frequency band, the frequency domain response of the slab track on the FVMP model are greater than those on the K-V model. At each reference temperature point, the response of the slab track on the FVMP model decreases with the decrease of the temperature. Therefore, in order to improve the accuracy of the track structure prediction, it is necessary to consider the temperature and frequency dependent properties of the damping layer.