The peak adjustment of seismic wave is often realized by the method based on the peak ground acceleration (PGA), while the peak acceleration of the design response spectrum in the current specification is the effective peak acceleration (EPA), and EPA is recommended for peak adjustment. Firstly, the meaning and internal relations of PGA and EPA were analyzed, and the existing EPA calculation methods at home and abroad were summarized. According to the different characteristics of bridge structure and building structure, the calculation formula of EPA for bridge structure time history analysis was modified. Secondly, the smoothing processing problem of seismic wave response spectrum in EPA calculation was studied, and three peak smoothing methods were proposed to analyze the value determination of relevant parameter and the advantages and disadvantages of each method. Finally, this method was applied to the time history analysis of a long-span cable-stayed bridge, and the displacement and internal force results of the structure based on PGA and EPA were compared. The results showed that the time history analysis results obtained by the peak adjustment method based on EPA were more reliable.