In order to improve the seismic performance of the trash rack structure, we studied the influence of the side concrete backfill height on the structure of the intake tower with long trash rack piers. A three-dimensional finite element model with different side backfill heights was established for the dynamic calculation of a tall intake tower, and the influence of the side concrete backfill height on the free vibration characteristics, displacement and stress of the intake tower were analyzed. Based on the calculation results, it is found that excessive backfill on the side of the tower adds extra compressive stress to some of the connecting beams of the trash rack piers exceeding their compressive strength, which will most likely result in beam fracture. On the other hand, the displacement of the tower across the river and the tensile stress of the connecting beams becomes larger without backfill on the side. An appropriate backfill height on the side can effectively reduce the stress of the long trash rack structure, limit the displacement across the river, and improve the overall seismic performance of the structure. The advisable range of the side backfill height of the intake tower with long trash rack piers proposed in this paper can be used as references for similar projects.