To fill the blank in the research on the dynamic performance of track structure under long-term service, the dynamic response study of China Railway Track System Ⅲ type slab ballastless track (CRTSIII SBT) under the action of fatigue for 30 million times and the parting between track slab and self-compacting concrete (SCC) was carried out. By establishing the finite element model of the CRTSIII SBT structure and taking the stiffness change of isolation layer and fastener under fatigue state and the parting during service as the research objects, combined with the full-scale model test, the dynamic response amplitude and vibration law of track structure was analyzed based on the finite element model of axle falling test method. The results show the following: (1) Under the fatigue load, the acceleration of rail and base increases obviously, the longitudinal tensile stress of SCC surface decreases, the longitudinal tensile stress of base surface increases, and the vertical stress of each layer of track structure increases as well. (2) Under the action of the parting, the dynamic response of each structural layer increases, and the change of acceleration and stress of each layer under the action point of axle falling is the most obvious. (3) The fatigue load will weaken the vibration damping performance of the track, and the parting will continue to develop under the action of the falling axle, resulting in partial or total failure of the SCC layer. Both of them will aggravate the dynamic response of the track structure and affect driving safety, which should be paid attention to during maintenance.