Ultraslow-spreading ridges are a novel class of spreading centers symbolized by amagmatic crustal accretion, exposing vast amounts of mantle-derived peridotites on the seafloor. However, distinct magmatic centers with high topographies and thick crusts are also observed within the deep axial valleys. This suggests that despite the low overall melt supply, the magmatic process interacting with the tectonic process should play an important role in crustal accretion; however, this has been obscured due to the lack of seismic images of magma chambers. Using a combination of seismic tomography and full waveform inversion of ocean bottom seismometer data from the Southwest Indian Ridge at 50°28′E, we report the presence of a large low-velocity anomaly (LVA) ∼4–9 km below the seafloor, representing an axial magma chamber (AMC) in the lower crust. This suggests that the 9.5-km-thick crust here is mainly formed by a magmatic process. The LVA is overlain by a high-velocity layer, possibly forming the roof of the AMC and defining the base of hydrothermal circulation. The steep velocity gradient just below the high-velocity layer is explained by the ponding of magma at the top of the AMC; this could provide the overpressure for lateral dike propagation along the ridge axis, leading to a complex interaction between magma emplacement, tectonic, and hydrothermal processes, and creating a diversity of seafloor morphology and extremely heterogeneous crust.