This article used FLAC^3D finite difference software to study the dynamic response rules of the new cutting bed structure with a new type of waterproof and drainage structure layer set in the bedding. Past studies have proven that a new bed ballast and a new type of waterproof and drainage structure can significantly contribute to the attenuation of dynamic stress. A new type of waterproof and drainage structure layer on vertical dynamic stress and shear stress attenuation can enhance the dynamic stability of the bedding structure, whereas a new bed structure can more effectively control bed dynamic displacement. New bed vibration velocity and acceleration decrease with the increase of depth. Meanwhile, the ballast of vibration velocity and the ensuring acceleration attenuation effect are obvious. The numerical simulation results and in-situ measurement data reveal a matching physical discipline at the vibration velocity and dynamic stress of the new cutting bed structure, indicating that both values decrease along the depth direction. The study's findings can be used and referenced for the design, construction, and dynamic response study of high-speed railway cutting subgrades in special soil areas.