Nishinoshima is located approximately 65 kilometres (35 nmi) northeast of the Honshu coast. The island is of volcanic origin, with deeply indented coastline of 117 kilometres (73 mi), and with its highest point at the peak of Takuhiyama 452 metres (1,483 ft) above sea level. The Matengai cliffs on the west coast of the island are the highest in Japan, at 257 metres (843 ft).
The climate of Nishinoshima is classified as a humid subtropical climate (Köppen climate classification Cfa) with very warm summers and cool winters. Precipitation is abundant throughout the year.