The museum building, constructed largely of local Okinawan limestone, was designed with the imagery of Okinawa's gusuku (castles) in mind.

The Natural History section of the museum is entered via a glass-floored walkway designed to look as though one is walking over coral, approaching an island.

[3] A large wrap-around screen shows short films about the geological origins of the Ryukyu Islands and about its natural environment, flora, and fauna.

[4] The History section is organized around a large map of the Ryukyu archipelago projected onto the floor and connected into a number of computer terminals allowing visitors to explore aspects of individual islands, including satellite photographs of famous sites, native flora and fauna, and local culture.

In addition to the main exhibit halls, cafe, museum shop, and auditorium, the museum includes an extensive library, and a "Hands-On Experience Room" (ふれあい体験室, fureai taiken shitsu) where visitors can explore aspects of Okinawa's natural environment and folk culture in a hands-on manner, including traditional clothing, musical instruments such as the sanshin, and a variety of puzzles and games.