The key issues in designing ballastless track for high-speed railway bridges are to reduce maintenance and improve track smoothness by understanding fatigue damage characteristics. This paper is based on the principle of bridge-rail interaction and train-track-bridge coupling dynamics, the refined simulation model of bridge-CRTS I Bi-block ballastless track system is established by using the finite element method. The longitudinal force distribution law of CWR (Continuously Welded Rail) and the dynamic response characteristics of coupling systems are studied, based on the Miner rule and S-N curve. The fatigue characteristics of ballastless track system laying on long-span bridge under the dynamic train load and the effect of ballastless track system design parameters changes on fatigue characteristics are discussed. The results show that the extreme values of longitudinal force of CWR all appear in the middle of the bridge span or near the bridge bearing, and attention should be paid to the strength checking of CRW laying on long-span bridge. Under the dynamic train load, the fatigue life curve of rail on the bridge is relatively smooth and the minimum life of rail which is laying on continuous bridge decreases from 27.1 years to 17 years that which is laying on cable-stayed bridge. The life curve of track plate laying on continuous bridge is relatively smooth, and the life curve of track plate laying on cable-stayed bridge is related to the stiffness of elastic cushion, which decreases in a stepped manner, and there will be no fatigue failure on the track plate during service. The life curve of the baseplate is related to the type of bridge, the minimum life value of the baseplate appears near the bridge bearing, and there will be no fatigue failure on the baseplate during service. Increasing the stiffness of elastic cushion can effectively improve the fatigue life of track plate, and increasing the vertical stiffness of fasteners can enhance the connection between rail and track plate and improve the fatigue life of rail. The increase in train speed will increase the dynamic stress amplitude of track structure and reduce the fatigue life of the rail.