The invention discloses a ballastless track-structured waterproof vibration-reducing flexible protecting structure and a paving method thereof. A waterproof linking layer and a buffer protecting layer are paved between the bottom of a ballastless track foundation plate and the top surface of a surface layer/bridge deck slab of a roadbed in a full-width manner. According to the ballastless track-structured waterproof vibration-reducing flexible protecting structure, by virtue of the linking layer and the buffer protecting layer which are paved on the full fracture surface, the overall stereoscopic water proofing and the integrality are realized; by regulating the dynamic modulus, the damping characteristic and the deformation adaptability of an asphalt concrete protecting layer by virtue of a special modifying enhancer, the rigidity matching and buffer vibration reducing functions are realized; and by enhancing the load diffusivity, the fatigue durability and the water damage resistance of asphalt concrete by virtue of the special modifying enhancer, the problems of premature failure, interlayer slurry extruding, disengaging, even frost heaving and the like of waterproof layers of existing ballastless track roadbeds are effectively solved, the integrality, the smoothness, the uniformity and the long-term stability of a lower base structure of a track are improved, and good and stable support is provided for a ballastless track plate, so that the fatigue life of the track plate is prolonged. The ballastless track-structured waterproof vibration-reducing flexible protecting structure is a long-lasting protection scheme.