Abstract: Aiming at the critical issue of seismic response aggravation and deformation pattern evolution in shield tunnels caused by non-homogeneous soil-induced ground motion amplification and deformation non-uniformity, this study takes a cross-river tunnel project in the lower reaches of the Yangtze River as the engineering background. Considering the dynamic nonlinearity of riverbed soil and the refined assembly of segments, a 3D refined finite element model with a longitudinal length of 500 m was established. The effects of seismic wave characteristics and the shear wave velocity ratio of adjacent soil layers on the failure mechanism and deformation mode of tunnels crossing longitudinally heterogeneous ground were systematically investigated. The results indicate that: under seismic action, the tunnel exhibits significant longitudinal non-uniform deformation, with the peaks of longitudinal joint opening and staggering concentrated on the soft soil side near the strata interface. The tunnel manifests a distinct "S-shaped" bending deformation at the interface, and the zone significantly affected by the abrupt change in strata extends to a range of 5 times the tunnel diameter (5D) into the soft soil side. Furthermore, the damage to the segmental concrete evolves asymmetrically: damage in the soft soil section is primarily concentrated in the conjugate directions of the cross-section, whereas in the stiff soil section, it is focused near the arch springings. The research findings provide a reference for the anti-seismic design of cross-river tunnels in heterogeneous ground.