It is particularly important to study the seismic response and loss cracking law of pumping station outlet tower structure under strong earthquake. Based on the regional characteristics and operation of an electric power irrigation pumping project， a three-phase coupling finite element model of water-structure-foundation is established by numerical simulation and modal identification. The results show that the main damage locations of pumping station outlet tower under earthquake are the bottom bent-pier contact position and the middle ring beam-diaphragm contact position. With the increase of inertia force （peak acceleration is 0.4g）， damage begins to occur in this part， and the damage develops upward along the bent. When the peak acceleration reaches 0.6g， the damage location range increases， and damage occurs in the two-storey bent and partition of tower structure， with damage reaching 0.970 and compression damage reaching 0.506 8. This study can provide reference for dynamic damage analysis of similar structures.