The museum displays Siebold's medical instruments, botanical specimens, and ethnographic collections that showcase his scientific work and cultural research in Japan. Visitors can view original documents, botanical illustrations, personal belongings, and artifacts from his time in Nagasaki. The museum features reconstructed sections of his residence and school at Narutaki Juku, giving insight into the 19th-century learning environment. The surrounding garden contains plants associated with his botanical studies, providing a living exhibition of his scientific contributions to understanding Japanese flora.