This study investigates the influence of rail bottom structures (RBSs) on the train-induced dynamic responses of large-diameter shield tunnels and surrounding strata. The case study is conducted on the Chongtai Yangtze River Tunnel. Model testing and numerical simulations are performed to evaluate the effects of RBSs, train speeds, and operating conditions on tunnel-stratum dynamic behavior. The main findings are summarized as follows: (1) The train-induced dynamic responses by the tunnel and adjacent strata are relatively small. The measured accelerations at the arch bottom, crown, and box culvert top of the tunnel are 0.065, 0.400, and 0.910 m/s², respectively. The maximum additional tensile and compressive stresses induced in the surrounding strata are 2.600 and 7.540 kPa, respectively. (2) The two RBSs exhibit similar cross-sectional distribution characteristics of dynamic responses. The RBS primarily affects the magnitudes, rather than the spatial distribution pattern, of the dynamic responses in the tunnel structure and surrounding strata. (3) The influence of the RBS is primarily confined to the region beneath its bottom surface, while its effect beyond this zone is negligible. At the edge of the RBS, the maximum differences in tunnel dynamic response and stratum reaction are 0.013 m/s² and 0.130 kPa, respectively. (4) Within the tunnel structure, the dynamic responses at all measurement points increase with increasing train speed, with points closer to the vibration source exhibiting higher sensitivity. In the surrounding strata, the dynamic response decreases with increasing train speed at points above the arch waist, whereas it increases at points below the arch waist. Among the measurement points, the foundation base exhibits the highest sensitivity to train speed, while the arch waist shows the lowest sensitivity.