AbstractInvestigating heterogeneous structures beneath active volcanoes is important for better understanding of volcanic activity and improved mitigation of volcanic risk. In central Japan, Hakone volcano has recently shown shallow earthquake swarms and deep low‐frequency earthquakes (DLFEs), which are probably related to geothermal or deep magmatic activity. In order to image the feeding system beneath this volcano, we estimate 3‐D P wave attenuation structure using waveform data recorded at permanent and densely distributed temporary seismograph stations. We first determine corner frequencies of the earthquakes and then perform a joint inversion to obtain attenuation terms (t*) and site responses. Values of t* are finally inverted to estimate the attenuation structure to a depth of 50 km. High‐attenuation zones at depths ≤5 km suggest that fracture zones are permeated with hydrothermal fluids. A high–strain rate zone revealed by geodetic observations is spatially correlated with a high‐attenuation volume at depths of 5–10 km, suggesting that the anelastic deformation is dominant in the high‐attenuation zones. A subvertical volume of moderate attenuation that is imaged at depths of 10–20 km beneath Hakone volcano is connected to the top of a zone of partial melting beneath Mt. Fuji at depths ≥30 km through a subhorizontal channel at a depth of ~25 km. DLFEs in the lower crust and fluid‐related activity such as earthquake swarms in the upper crust occur in this volume. The zone is thus interpreted as a fluid‐bearing pathway, which allows the rise of magmatic fluids to Hakone volcano.