During the past two decades, five magnetotelluric studies conducted at Kusatsu–Shirane Volcano (KSV) in central Japan have revealed the resistivity structure of the entire edifice from the vicinity of the active crater lake to a depth of about 10 km below sea level (bsl). The resistivity structure models obtained by these studies are reasonably consistent with each other and are characterized by three distinctive conductive regions: (1) a conductive layer with a thickness of about 0.5–2 km and distributed over a wide area near the surface of Mt. Shirane and the southeastern flank is interpreted as a smectite-rich clay layer or acidic fluids; (2) an extremely low-resistivity region widely distributed beneath the summit area at depths of about − 0.5 to 4 km bsl (1.5–6 km below the summit) is interpreted as a zone containing high-salinity magmatic fluids; (3) a moderately conductive (10–20 Ωm) region extending from the bottom of region (2) to a depth of ~ 10 km bsl is interpreted as a partially molten zone containing degassing magma. In particular, the conductor of region (2) is considered to be the common fluid source of crater lake water and most hot springs in KSV and therefore a key structure for understanding the magmatic–hydrothermal system of KSV. For example, both the recent unrest events beneath Mt. Shirane and the 2018 eruption of Mt. Motoshirane can be explained by the expulsion of high-temperature volcanic fluids from this conductor. The fact that two volcanic cones, Mt. Shirane and Mt. Motoshirane, which exhibit contrasting volcanic activity characteristics, share a common fluid source indicates the importance of geophysical exploration and monitoring of targeted deep magmatic–hydrothermal systems for volcanic hazard assessment.