Transform plate boundaries, one of the key elements of plate tectonics, accommodate lateral motions and produce large earthquakes, but their nature at depth remains enigmatic. Using ultra-long offset seismic data, here we report the presence of a low-velocity anomaly extending down to ~60 km depth beneath the Romanche transform fault in the equatorial Atlantic Ocean. Our result indicates the presence of deep penetration of water leading to extensive serpentinization down to 16 km, followed by a shear mylonite zone down to 32 km over a low-temperature water induced-melting zone, elevating the lithosphere-asthenosphere boundary and hence thinning the lithosphere significantly beneath the transform fault. The presence of a thinned lithosphere and the melt underneath could lead to volcanism, migration and mixing of the water-induced melt with the high-temperature melt beneath the ridge axis, and small-scale convections beneath transform boundaries. Hence, a thinned lithosphere will have a major impact on the dynamics of ridge-transform system, and will influence the evolution of fracture zones and oceanic lithosphere.