Magnetotellurics (MT) is an important geophysical method for exploring geothermal systems, with the Earth resistivity obtained from the MT method proving to be useful for the hydrothermal imaging changes of the system. In this research, we applied the MT method to map the geothermal system of the Seulawah Agam volcano in northern Sumatra, a site intended for the construction of a geothermal power plant with an estimated energy of 230 Mwe. Herein, 3D MT measurements were carried out, covering the entire area of the volcano and the various intersecting local faults from the Seulimeum segment in the NW–SE direction. Based on Occam 2D inversion, a conductive anomaly (<10 ohm·m) near the surface was identified in response to specific manifestation areas, including the Heutsz crater on the northern side and the Cempaga crater on the southern side. A further conductive anomaly was also found at a depth of 1 km, which was presumably due to a clay cap layer covering the fluid in the reservoir layer below the surface, where the manifestation areas are formed at various locations (where faults and fractures are found) owing to the fluid in the reservoir rising to the surface. The MT modeling also revealed that the reservoir layer in Seulawah Agam lies at a depth of 2 km with a higher resistivity of 40–150 ohm·m, which is the main target of geothermal energy exploration. At the same time, the heat source zone where magma is located was estimated to lie in two locations, namely, on the northern side centering on the Heutsz crater area and the southern side in the Cempaga crater area. A clear 3D structure obtained via Occam inversion was also used to visualize the hydrothermal flow in the Seulawah Agam volcano that originates from two heat source zones, where one structure that was consistent across all models is the conductive zone that reaches a depth of 5 km in the south in response to the regional faulting of the Seulimeum segment. Based on the MT research, we concluded that the volcano has the geothermal potential to be tapped into power plant energy in the future.