The dislocation of the active fault zone altered the stress distribution and geometry of the track structure in the tunnel, which in turn affected the safety and stability of the train operation. Polyurethane-solidified track bed (PSTB) is suitable for sections crossing through active fault zones due to its excellent serviceability and adaptability to deformation. In this study, the stress and deformation response induced by active fault dislocation are investigated for this novel track structure. The corresponding deformation of track structure is subsequently introduced into a vehicle-track dynamics model to calculate the train operation safety index. The study examines the impact of fault displacement on railway track structures, revealing significant vertical deformation in rails that corresponds to the displacement magnitude. The effects are mainly confined to the active fault zone and its immediate surroundings, with variations depending on the fault zone’s structural characteristics. Key factors such as larger displacements, steeper fault angles, and narrower fault zones increase stress on track components, particularly the wide sleeper, which is prone to cracking and represents a structural vulnerability. Higher fault displacement, narrower zones, steeper angles, and increased train speeds elevate derailment risks and wheel load reduction rates, potentially exceeding safety limits. To ensure safety under typical fault conditions, train speeds should not exceed 250 km/h for PSTB with a 40 mm displacement and a 60° fault angle. These findings provide critical guidance for railway construction in fault-prone areas.