ABSTRACT Canyons have a significant influence on near-fault earthquakes, and near-fault earthquakes exhibit strong amplitude and large spatial variability. In turn, this causes the damage and deformation of the high-speed railway (HSR) bridge-track system with unequal pier heights, which affects the normal service of the unequal pier heights bridge and the safe running of the train. This study investigates the damage and deformation of HSR bridge-track systems with unequal pier height in canyon areas under near-fault seismic based on FK (frequency wavenumber)-FE (finite element) method. It aims to offer suggestions for seismic design in canyon regions of HSR unequal pier height bridges. First, a finite fault kinematic hybrid source model and a canyon site model were established, and the FK-FE hybrid method was employed to simulate the three-dimensional (3D) site motion considering the full process of the seismic source-propagation medium-complex site (SSPC). Then, the influence of near-fault earthquakes and the canyon topography on the spatial distribution of near-fault ground motions were analyzed, and the non-uniform near-fault seismic excitation at the bottom of each pier considering the canyon topography effect was obtained. Finally, a nonlinear dynamic FE model of the HSR bridge-track system was established, and its damage patterns and mechanism in canyon near-fault earthquakes were analyzed. The results indicate that near-fault earthquakes in the canyon exhibit significant vertical and sliding effects with significant spatial variability and the FK-FE method can provide more accurate ground motion input. The seismic damage to HSR bridge-track systems increases as the fault distance decreases, and topography effects further aggravates seismic damage to HSR bridges. Moreover, vulnerable areas in the track system are often found at girder ends. Therefore, for HSR bridges in canyon regions, seismic input needs to comprehensively consider the effects of near-fault earthquakes and topography, with post-earthquake focus on damage assessment at girder ends.