A controlled source audio frequency magnetotelluric (CSAMT) survey was conducted over Showa-Shinzan Dome at Usu Volcano, Hokkaido, Japan, in order to investigate its internal structure. The Showa-Shinzan Dome (800-1000m across, 350m high) is a partly extruded cryptodome that formed in AD 1943-45 due to the uplift of pre-existing rocks and sediments by the intrusion of dacitic magma. The dome comprises a flat-topped cryptodome called ‘Yaneyama’ and a dacitic lava dome projecting above the Yaneyama cryptodome. The CSAMT survey was carried out on a 1600-m-long line that crosses the Showa-Shinzan Dome in an east-west orientation. Two-dimensional inversion of the CSAMT data revealed the resistivity structure at depths less than 1000m beneath the dome. The resistivity structure suggests the existence of a sub-spherical dacite intrusion (resistivity 50-130Ω・m; ～400m across) below the summit of the Showa-Shinzan Dome. The dacite intrusion may represent the solidified dacitic magma emplaced in AD 1943-45. The Yaneyama cryptodome only comprises pre-existing rocks and sediments uplifted by the intrusion of dacite magma. The upper zone of the Yaneyama cryptodome consists of the Usu Somma Lava (＞100Ω・m), whereas the lower zone consists of Quaternary pyroclastic flow deposits and sedimentary rocks (＜30Ω・m), such as the Toya pyroclastic flow deposits, the Fukaba Formation, the Takinoue welded tuff, the Sobetsu pumice flow deposits, and the Yanagihara Formation. There is no dacite intrusion beneath the Yaneyama cryptodome. This structural model is consistent with the distribution of active fumaroles on the Showa-Shinzan Dome, and also with historical records of dome growth. The geophysical data provide new insights into the formation mechanism of the Showa-Shinzan Dome.