The Endere site, in the Taklamakan desert, was an important place linking the East and the West on the Silk Road during the ancient times. A remarkably large pagoda in the ruin symbolizes the architecture of the site. During the passed thousand years, the pagoda has been seriously damaged due to natural and artificial factors. The results of an on-site survey show that the main causes of damage are wind erosion, water erosion, crevices, collapse and artificial holes, among which wind erosion is the most fatal one. Considering the environment of the pagoda and the Principles for the Conservation of Heritage Sites in China, it is necessary to reinforce the base of the structure and fill the artificial holes. It will be useful in the long-term preservation of the pagoda and providing a good foundation of large-scale conservation efforts in the future.