Axial Seamount is the most volcanically active site of the northeast Pacific, and it has been monitored with a growing set of observations and sensors during the last two decades. Accurate imaging of the internal structure of volcanic systems is critical to better understand magma storage processes and to quantify mass and energy transport mechanisms in the crust. To improve the three‐dimensional velocity structure of Axial Seamount, we combined 469,891 new traveltime arrivals, from 12 downward extrapolated seismic profiles, with 3,962 existing ocean‐bottom‐seismometers traveltime arrivals, into a joint tomographic inversion. Our approach reveals two elongated magma reservoirs, with melt fraction up to 65%, representing an unusually large volume of melt (26–60 km3), which is likely the result of enhanced magma supply from the juxtaposition of the Cobb hot spot plume (0.26–0.53 m3/s) and the Axial spreading segment (0.79–1.06 m3/s). The tomographic model also resolves a subsided caldera floor that provides an effective trap for ponding lava flows, via a “trapdoor” mechanism. Our model also shows that Axial's extrusive section is thinnest beneath the elevated volcano, where anomalously thick (11 km) oceanic crust is present. We therefore suggest that focused and enhanced melt supply predominantly thickens the crust beneath Axial Seamount through diking accretion and gabbro crystallization. Lastly, we demonstrate that our three‐dimensional velocity model provides a more realistic starting point for relocating the local seismicity, better resolving a network of conjugate outward and inward dipping faults beneath the caldera walls.©2018. The Authors.