Natural History Exhibition Hall displays the natural history items including marine life, soil and rocks, and fauna and flora of Jeju in a three-dimensional way. It is divided into Ecology Hall of Marine Life, Soil and Rock Exhibition Hall, and Land Ecosystem Hall.
Ecology Hall of Marine Life displays 354 items of fish and shellfish collected from the coastal waters of Jeju including a 4.5m long regalecus russelli, a whale shark, an abalone, and a diamond back squid.

Soil and Rock Exhibition Hall displays shellfish fossils, fossil bird footprints, and Manjang Cave miniature and shows the Jeju formation process and volcano eruption scenes.

Land Ecosystem Hall has six areas such as costal wetland, indeciduous broad-leaf forest, grassland, deciduous forest, needle-leaf forest, and high mountain shrubbery ( Baeknok Lake area), in which all of fauna and flora specimens in Jeju are displayed. The specimens of spot-billed ducks, white-backed woodpeckers, brown-eared bulbuls, milkweed butterflies and fireflies are displayed in a dynamic way. It shows the film on Snakes and preserved plants in Jeju. It also displays 11 mushrooms, 10 tangerines, 512 insects and 26 animal bone structures.