The fling-step effect caused by near-fault ground motion induces a step-like permanent displacement of the ground surface, which decays sharply with increasing fault distance, leading to varying degrees of ground motion at each supporting point of the bridge structure. In this context, multi-span long-span bridges exhibit echelon displacement of the main beam and a more complex internal force response compared to ordinary bridges. To investigate the seismic response characteristics of multi-span long-span continuous girder bridges under near-fault ground motion, this study is based on the permanent displacement attenuation model. The main bridge of the Hongyazi Yellow River Bridge in Shizuishan City, consisting of 16 spans, is taken as the research object. Using OpenSees software, a finite element model for the dynamic analysis of the multi-span long-span continuous girder bridge was established, and its structural dynamic characteristics were compared with the natural vibration test of the actual bridge. Based on simulated ground motions that consider the permanent displacement attenuation effect and spatial variability, the seismic response of the key components of the near-fault multi-span long-span continuous beam bridge is examined. The results indicate that under near-fault ground motion considering the attenuation effect of permanent displacement, the main girder of multi-span long-span bridges frequently deviates from the axis in different directions, ultimately resulting in residual deformation of the main girder post-earthquake. The permanent displacement attenuation effect increases the maximum bending moment response at the pier bottom and causes uneven internal force distribution in the bridge. Ignoring this effect can lead to overestimation of bearing deformation.