Assessing the fragility of intake towers using a single damage index does not allow for accurate evaluation of the potential for structural damage under seismic conditions. In this study, based on the probabilistic seismic demand analysis method, the effects of ground motion intensity on maximum displacement, local damage index, and global damage index are considered, and the seismic fragility of an intake tower structure is analyzed. First, 10 natural ground motion records were selected from the ground motion database (PEER) and 2 artificial seismic waves were synthesized. These seismic waves were amplitude-modulated for incremental dynamic analysis (IDA). The trends of the IDA curves were analyzed to divide the performance levels of the intake tower structure. Furthermore, a two-dimensional fragility curve for the intake tower structure was plotted in this study. The maximum displacement in the direction of parallel flow and the damage index were taken into account in the two-dimensional fragility curve. The results show that, under the designed seismic acceleration, the two-dimensional fragility curve for the intake tower structure was lower than the one-dimensional curve. This indicates that the seismic design based on the one-dimensional performance index was unstable. This provides a theoretical reference for seismic optimization design and the strengthening of intake towers. Therefore, it is recommended to use multidimensional fragility analysis to study the seismic performance of intake tower structures in seismic design.