Current situation and accumulated development of archaeological sites have very high impacts on the preservation value of the site. This research set 3 archaeological sites in Taiwan as study areas. Assessment of the degree of destruction of cultural layers due to land use change and morphological change were conducted with aerial photographs (1976~1978; 2016~2017) and digital aerial survey technology. The results showed that the archaeological sites were all seriously influenced due to the high land use intensity between 1976~2017. Morphological changes caused by human cultivation and engineering construction were main causes of site destruction, especially in private lands. Therefore, urban planning methods for land acquisition or land regulation are necessary. The prediction model of the destruction degree of the cultural layers of the site developed by the research team has also achieved good predictive ability. In the future, this technology can be applied to improve the effectiveness of archaeological sites management and effectively review the problem factors.