The Alishan Ecological Education Center is located within the Alishan National Forest Recreation Area, but its conservation concern areas include three sites: the Taiwan Aspidistra Nature Reserve, the Tashan Important Wildlife Habitat, and the Lulinshan Important Wildlife Habitat. Staff from the Alishan Station of the Forestry and Nature Conservation Administration have long been involved in environmental monitoring and resource surveys of the surrounding protected areas. They have also conducted habitat restoration work on the Alishan salamander and the Taiwan Aspidistra, achieving significant results over the years. To raise public awareness of the importance of protected habitats and species conservation, the center uses the protected species—the Alishan salamander and the Taiwan Aspidistra—as the main theme of the museum, explaining the research process and results.

To promote nature conservation concepts and help visitors understand the natural ecology of Alishan, the Chiayi Branch of the Forestry and Nature Conservation Administration renovated the old Alishan Station and other old buildings into the Alishan Ecological Education Center, the Taiwan Aspidistra Ecological Story Hall, and the Alishan Salamander Hall.