Current research on the dynamic response of building structures under the mainshock-aftershock sequence indicates that aftershocks after the mainshock often cause the accumulation of structural damage, resulting in structural crack extension or even collapse. However, the mainshock-aftershock sequence is seldom used in the analysis of earthen sites. In the study, the central pagoda of Ta'er Temple in Suoyang City was investigated. Six natural ground motion records were selected with the target spectrum matching method, and the dynamic responses of the structure under the action of single mainshock and mainshock-aftershock sequence were studied. Results indicate that the change trends of acceleration and displacement responses along the height of the pagoda are basically the same under the action of mainshock and aftershock. The maximum values of acceleration and vertical displacement are located at the apex of the pagoda, whereas the maximum horizontal displacement is located at the combination of the mantle body and pagoda body. The aftershock will expand the scope and degree of the plastic damage caused by the mainshock, especially in the severely damaged parts. Through the above analysis, the weak positions of the central pagoda of the Ta' er Temple are exposed, and improvement measures, such as support reinforcement in suitable parts, are proposed.