<p>This paper investigates the dynamic responses and damage mechanisms of shield tunnels under the coupling effects of near-fault ground motions and karst geology. Three types of near-fault ground motions—forward directivity effect, fling-step effect, and non-pulse—are systematically analyzed in conjunction with two typical karst configurations: lateral karst cavities and bottom filled karst caves. A multi-section monitoring system is employed to quantify the spatial correlations among deformation patterns, stress characteristics, and damage severity. The results demonstrate that pulse-like characteristics and karst configurations synergistically govern structural dynamic responses and damage patterns. Under forward directivity effect and non-pulse motions, the tunnel exhibits vault settlement and bottom uplift, while the fling-step effect induces abnormal deformation patterns (vault uplift and bottom settlement) due to their significant pulse-like characteristics. Under non-pulse motions combined with lateral cavities, tunnel stress increases with distance from the tunnel center. In contrast, stress magnitudes decrease with distance from the center in all other cases, except under fling-step motions combined with bottom filled karst caves. Under fling-step motions with prominent pulse characteristics, lateral cavities weaken the surrounding rock support. This serves as the primary cause of damage shifting to the haunch. Conversely, for bottom karst caves, the low elastic modulus of the infill materials reduces the structural bearing capacity, which is the main driver of damage migration to the bottom. These findings establish a theoretical foundation for optimizing seismic design, enhancing disaster mitigation strategies, and guiding rehabilitation measures in karst tunnel engineering.</p>