We present a three‐dimensional crustal structure of a magmatically robust segment of the ultraslow‐spreading Southwest Indian Ridge at 50°28'E based on tomographic inversions of an ocean bottom seismometer data set. Our results show an upper crustal low‐velocity band in the axial zone, which is attributed to increased porosities due to active extensions, leading to anisotropy in the upper crust with a fast direction subperpendicular to the spreading direction. In the lower crust, the results reveal a round‐shaped low‐velocity anomaly at the segment center, indicative of high temperatures and/or a small amount of melt, suggestive of the presence of an axial magma chamber. At the midcrustal depth, an along‐axis asymmetry is observed with respect to the segment center. While a small low‐velocity anomaly indicates lateral magma redistribution toward the western segment end, the deep‐penetrating low velocities and high velocity gradients toward the eastern end suggest that the crust is colder and contains a thicker fractured layer. This asymmetry occurs very close to the axial magma chamber (<5 km) and seems to be related to the fact that the oblique‐spreading domain at the eastern end offsets the ridge axis by a larger distance than that at the western end. We suggest that an along‐axis deep‐penetrating hydrothermal circulation develops on the east side of the axial magma chamber, in response to the rapid change from orthogonal‐ to oblique‐spreading domains and cools the crust.