We conducted a broadband magnetotelluric (MT) survey along a north-south transect across Unzen graben, Japan. The MT survey line is located ~ 2 km west of the most recent lava dome and consisted of 27 stations along a 9-km profile. We estimated the 3-D resistivity structure and correlated it with the seismic reflection structure obtained by the same survey line as in the present study. The best-fit resistivity structure shows an upper resistive layer underlain by a moderately conductive layer. The resistive layer, which is interpreted as a cold groundwater zone, is cut by four faults marked by their relatively high conductivity. The underlying layer, which is interpreted as a hydrothermal-waterrich layer, also shows relatively conductive values near the faults. By assuming that the faults are imaged as relatively conductive zones, we infer the dip and depth extent of fracture zones around the faults. Beneath the Chijiwa Fault, which is the longest and most active fault of Unzen graben, the dominant conductor (C1) has a width of 2 km and extends down to below 4 km depth. C1 corresponds to a zone of strong seismic reflection and is located close to one of the pressure sources causing surface deformation. In this study, we interpret C1 as a network of fractures generated by the Chijiwa Fault to which magmatic volatiles are supplied from a deeper pressure source. Given that C1 extends to a greater depth and its resistivity is lower than other conductive zones, it is possible that earthquakes have occurred repeatedly on the Chijiwa Fault. In the center of the study area, we identify a vertically oriented body of high resistivity (R1) that corresponds to a zone of low seismic reflectivity. We interpret R1 as a cooled dyke complex that may have acted as a volcanic conduit.