The Epang Palace Site was selected as a typical example of a large-scale earthen archaeological site, to investigate the effects of plants on it. The combination of on-site investigation using the transect method, image analysis and soil sampling was carried out to analyze the distribution of the planting area, root-induced cracks and soil characteristics. The results show that the main cause of damage to the site is plant roots, which, in combination with rain erosion, weathering and human damage, seriously threaten the site. The root-induced cracks and the effects of plant roots on the soil environment from species such as Ziziphus jujuba Mill. and Ailanthus altissima play a key role among all the various threats to the soil ruins of Epang Palace. The types of damage mainly include earth cracks and collapses, shrinkage of wall bases, surface exfoliation, and many gullies and holes which are quite unique for earthen archaeological sites in semi-arid areas. This research could help not only to reveal the mechanism of planting effects on earthen archaeological sites, but also provide theoretical and technical support for plant selection for site conservation.