The standard does not give a general range the selection of backfill height of high intake tower, the influence of backfill on the stress of tower body is generally considered; however, the stress at the junction of backfill and basement is less involved. In this study, the three-dimensional finite element model of the stable intake tower was established using the ANSYS finite element analysis theory, and the dynamic response of the intake tower under earthquake was calculated using response spectrum method. The natural frequency, displacement, tower stress, and the degree of influence of joint stress at backfill intersection with bedrock were compared and analyzed. The results showed that the backfilling behind the tower can effectively increase the natural frequency of the tower in certain range, and improve the displacement and stress of the tower. The stress value at the interface between backfilling concrete and bedrock increased slightly. When the backfilling height behind the tower exceeded a certain value, the improvement effect of increase of backfilling height on the natural frequencies, displacements and stresses gradually weakened. The stress at the interface between Backfill Concrete and bedrock behind the tower increased sharply. All in all, the reasonable backfill height of this kind of intake tower is about 0.64 times of the tower height.