AbstractHigh‐resolution images of subsurface structures are necessary to understand the transport processes of crustal fluids from deep magma sources and their relationship to earthquake swarms in active volcanic regions. Based on a seismic tomography approach, we have developed a new model for the magma‐hydrothermal system beneath Hakone volcano, central Japan, where shallow earthquake swarms and crustal deformation associated with inflation of an open‐crack source are often observed. By applying travel‐time data for local earthquakes to a tomographic inversion, we obtained highly resolved seismic velocity structures that show a region of low P‐wave velocity (Vp), low S‐wave velocity (Vs), and high Vp/Vs ratios at depths of 10–20 km beneath the volcano, corresponding to the location of the open‐crack source. We suggest that the high Vp/Vs ratios represent a deep magma chamber with a high concentration of melt and/or fluids. Deep low‐frequency earthquakes, located just beneath this high Vp/Vs zone, may indicate that magmatic fluids are supplied from below. Above the high Vp/Vs zone, a region of low Vp, low Vs, and low Vp/Vs ratios exists at depths of 3–10 km, suggesting the presence of crack‐filled water or CO2 supplied from the inferred deep magma chamber. Many earthquake swarms occur in this low Vp/Vs zone, indicating that crustal fluids play an important role in generating the swarms. Similar relationships between magma reservoirs, overlying hydrothermal systems, and swarm activity have been reported from other volcanic areas and thus may be a ubiquitous feature beneath active volcanoes.