The full-section asphalt concrete waterproof layer (FACWL) has garnered significant attention for its outstanding ability to reduce frost heave and thaw-related weakening in railway track beds, particularly in seasonally frozen regions. To explore the dynamic properties of the FACWL, a fractional-order constitutive model was utilized to characterize the viscoelastic behavior of asphalt concrete. Additionally, a vehicle–track coupled finite element (FE) model and the numerical approach incorporating the fractional-order constitutive model were developed and validated via experimental and field testing. Simulation results indicate that applying the FACWL reduces the vertical dynamic response of each structural layer, vertical peak accelerations across the subgrade surface layer exhibited reductions exceeding 30% in both positive and negative directions. Moreover, the tensile strain at the bottom of the FACWL remained relatively low, less than 100 με. Compared with conventional waterproof sealing layers, the viscoelastic nature of the FACWL facilitates energy dissipation, effectively decreasing the overall vibrational amplitude and vertical deformation within the track structure by more than 20%. Consequently, the FACWL plays a crucial role in ensuring the long-term stability of the subgrade and minimizing vibrations in the track system.