After a strong earthquake occurs, it can cause a certain degree of damage to the structure, and the strong aftershock effect can cause secondary damage to the already damaged structure. In this study, taking a actual project of intake tower in the district of western strong earthquake as an example, the acoustic unit is used to simulate the dynamic effect of reservoir water on the tower body, and the overall nonlinear model of the water-intake tower-foundation is established. Combined with the site and seismic motion characteristics of the engineering area, the seismic motion sequence of the main-aftershocks was constructed based on the statistical relationship between the main shocks and strong aftershocks, as well as the NGA seismic motion attenuation model. The effects of main shock, aftershock, and main-aftershock on the structural damage evolution of intake towers in strong earthquake zones were investigated separately. The results show that after considering the aftershock effect, the damage and failure of the intake tower structure intensify, and its dissipation energy and residual displacement increase by about 20%~25%. Compared with the main shock, the aftershock alone causes less damage to the tower structure. However, for the intake tower structure that is damaged after the main shock, the aftershock can cause larger secondary residual deformation of the tower.