Tori-shima was known to Japanese fishermen and mariners since at least the early Edo period, but was uninhabited aside from occasional shipwreck survivors.

In 1841, 14-year-old Nakahama Manjirō and four friends were shipwrecked on Tori-shima until rescued by the American whaleship John Howland commanded by William H. Whitfield.

Since the 1930s, the Yamashina Institute for Ornithology has taken a very active role in researching and attempting to preserve the local seabird species, especially the short-tailed albatross, which had been reduced to an estimated 50 birds by 1933.

Tori-shima, along with the other Izu Islands, is officially part of Tokyo Metropolis, and also falls within the borders of the Fuji-Hakone-Izu National Park.

Repeated volcanic eruptions in 1939 and 2002 have set the flora on Tori-shima back to initial stages in the ecological succession.

Plants such as Vitex rotundifolia and hydrangea are found near the shoreline, and Chrysanthemum pacificum and Japanese black pine in sheltered areas inland, but most of the central portion of the island remains as volcanic ash and rock.

The island is home to several tens of thousands of breeding pairs of Tristram's storm petrel and other birds such as Japanese murrelet, black-footed albatross, common kestrel, and blue rock thrush, but the short-tailed albatross population has been very slow to recover, with recovery hampered by the presence of large numbers of black rats, the only remaining mammal on the island, eating bird eggs.