Abstract: The effects of duration of the endurance time analysis on the seismic response of the underground structures are investigated. The typical two-story three-span subway station embedded in the sites of classes II and III is used as the prototype. The response spectra at the engineering bedrock is used as the target ones to develop six endurance time acceleration functions as the input motions for the nonlinear soil-structure interaction system. Using the results from the incremental dynamic analysis as the reference, the effects of time duration of the endurance time analysis on the seismic analysis of underground structures are significant. A formula to compute the optimal time duration based on the variations of earthquake ground motion energy measure, Arias intensity, with the target time is proposed and validated. It can be seen from the numerical results that endurance time acceleration functions with durations of 30 and 45 s are more favorable for the underground structures embedded in the sites of classes II and III, respectively. Moreover, the proposed formula for the optimal duration estimation is feasible for the seismic performance evaluation of underground structures in the above two site classes. The results from the endurance time analysis are more accurate when the total energy in the artificial endurance time acceleration function is close to the actual earthquake records.