Our seismic tomographic images characterize, for the first time, spatial and volumetric details of the subvertical magma plumbing system of Merapi Volcano. We present P- and S-wave arrival time data, which were collected in a dense seismic network, known as DOMERAPI, installed around the volcano for 18 months. The P- and S-wave arrival time data with similar path coverage reveal a high Vp/Vs structure extending from a depth of ≥20 km below mean sea level (MSL) up to the summit of the volcano. Combined with results of petrological studies, our seismic tomography data allow us to propose: (1) the existence of a shallow zone of intense fluid percolation, directly below the summit of the volcano; (2) a main, pre-eruptive magma reservoir at ≥ 10 to 20 km below MSL that is orders of magnitude larger than erupted magma volumes; (3) a deep magma reservoir at MOHO depth which supplies the main reservoir; and (4) an extensive, subvertical fluid-magma-transfer zone from the mantle to the surface. Such high-resolution spatial constraints on the volcano plumbing system as shown are an important advance in our ability to forecast and to mitigate the hazard potential of Merapi’s future eruptions.