We conducted a high-resolution aeromagnetic survey using an autonomously driven uncrewed helicopter that flew as low as several tens of meters above the ground along precise flight tracks with 1 m accuracy. The geomagnetic total intensity was measured by a total intensity magnetometer suspended beneath the helicopter at a ~ 50 m or less flight spacing over the entire caldera of Mt. Mihara, located on Izu-Oshima Island, Japan. From the observed geomagnetic data, we estimated high-resolution subsurface magnetization intensity. A high average magnetization intensity of 13.5 A/m was obtained for the entire caldera. The distribution of the magnetization intensity was not only consistent with the results of conventional airborne surveys, but it also had a high spatial resolution of less than 100 m. Highly magnetized areas were observed along the NW–SE lines that intersected the summit pit crater, Crater A, which is consistent with the principal stress direction of Izu-Oshima Island. These highly magnetized areas might be solidified magma that did not reach the surface during past eruptions. A large and deep-rooted weakly magnetized area was found just outside of the NE side of the central cone, which corresponds to the location of Fissure B, and the conduit must have been demagnetized at the previous event. Other weakly magnetized areas were also observed at the N, E, and SW sides around the pit crater. These regions correspond to the location of fumaroles in the crater. The high-resolution subsurface magnetization imaged by the autonomous uncrewed helicopter will be helpful for the mitigation of future eruption damage by enabling the assessment of potential fissure eruption areas.