Durations are defined as an essential component of the three primary characteristics of strong earthquakes, which exhibit a remarkable influence on the damage characteristics of a concrete dam body. However, when considering the distinctive definitions of a strong motion duration, the influence of several durations on the seismic analysis of gravity dams remains unclear. In addition, there is no specific conclusion on the optimal choice for the duration of a strong ground motion. The endurance time analysis (ETA) method, which is a high-efficiency seismic performance method, is widely used, because of the high precision and low computation effort when calculating the dynamic responses of structures. However, when using this method it is almost impossible to account for any one type of duration contribution. Therefore, a modified ETA algorithm to correct duration effects will be proposed in this paper based on the three existing types of durations, such as bracketed (T-b), uniform (T-u), and significant (T-s) durations. The dynamic response will be further corrected using a modified ETA method in the numerical application to the Koyna concrete gravity dam, which is one of the largest dams in Maharashtra state, India. A group of 20 endurance time acceleration functions (ETAFs) and 10 sets of two-dimensional (2D) artificial waves with three total durations will be synthesized through the same site design acceleration spectrum. Three types of indices that include the dissipation energy, damage, and deformation indices will be used to measure the seismic performance. The nonlinear analysis results will be compared with those from the ETA and quantitative analysis methods, which show that the modified ETA method could provide an effective estimation to monitor earthquake resistance and structural seismic performance with a certain safety margin. The influence of the duration of a strong ground motion could be considered in the modified ETA method, which could be further applied in practical engineering.