Earthen architecture is one of the oldest forms of construction. It is composed of construction materials made from unfired earthen materials, including adobe, rammed earth, and a host of other earthen components and construction techniques that vary with varying cultures and regions. Numerous single earthen sites remained in the northwest region of China. However, these cultural relics have not been preserved well. The physical and chemical properties, as well as the mineral compositions and textural characteristics of the soils, are the intrinsic factors that determine the form of weathering, whereas the natural environment is the driving force promoting the damage process. Among them, the structural failures induced by earthquakes are a form of the most serious problems which affect the preservation of the sites. It is worthwhile to provide any effort to achieve a convincing explanation of the distress causes and to propose interventions that are safe and respectful of the history of the sites. To better protect the single earthen sites, FLAC^3D software was applied to analyze the dynamic response of the Liufuzhai Watchtower under seismic loads and the seismic-induced displacement, stress and the acceleration amplification effect of seismic wave was investigated. The results indicate that the Watchtower produces a certain permanent displacement, which is mainly vertical displacement under seismic loads. Meanwhile, there is a tensile stress concentration which is close to the tensile strength in the fissure of the Watchtower. The amplification effect of seismic acceleration strengthens with the increase of height, especially for the vertical acceleration. The fissure has a strong adverse effect on the vertical displacement. Meanwhile, the acceleration amplification factor on the fissure is the largest. However, the fissure can weaken the amplification effect of adjacent points. This case study provides an innovative approach to predict the stability of cultural sites when an earthquake occurs; in particular, it is suitable for earthen sites in Northwest China.