The seismic performance of intake tower structure is of great significance to the safety and operation of hydropower stations. The seismic performance of the high-rise independent intake tower structure of Shapai Hydropower Station was analyzed and evaluated subjected to three endurance time accelerograms (ETAs). The calculation results were then compared with the incremental dynamic analysis (IDA) results under natural ground motions, and the comparisons of the top displacement, the base shear, and the seismic damage history of the intake tower were performed. The case study results showed that compared with IDA method, the endurance time method can better analyze the seismic response of the structure and match the mean value of IDA results. The endurance time method can get the structure response under different dynamic strengths by using less time-history analysis, and the calculation results are accurate and efficient, thus providing a new method for the seismic performance analysis of the water intake tower structure.