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Dynamic loads such as the train vibration load usually act on the shield tunnel lining in the long term, which could make the initial flaws in shield segment propagate and gradually weaken the robustness of the tunnel structure. In this paper, a three-dimensional numerical model of shield tunnel lining structure with the initial defect is built to study its dynamic reaction and fatigue crack propagation under the train vibration load. Furthermore, the damage to intact shield segment caused by train vibration load is studied by employing the rain-flow counting method and the Miner damage theory, and a rational fatigue life estimation for the concrete shield tunnel lining is finally made. Results show that crack propagation is influenced by both the train speed and train axle, the higher the train speed, the longer the final crack, and train axle has a larger influence than train speed on the crack propagation in shield tunnel segment. The shield tunnel lining structure of Nanjing Metro Line 5 can meet the demand of working for a hundred years under the current working conditions. [ABSTRACT FROM AUTHOR]