The origin of Hangai Dome, an unusual large-scale, high-elevation low-relief landform in central Mongolia, remains enigmatic partly due to lack of constraints on its underlying seismic structure. Using adjoint tomography—a full waveform tomographic technique—and a large seismic waveform data set in East Asia, we discover beneath the dome a deep low shear wave speed (low-V) conduit indicating a slightly warmer (54 K to 127 K) upwelling from the transition zone. This upwelling is spatially linked to a broader uppermost mantle low-V region underlying the dome. Further observations of high compressional to shear wave speed ratios and positive radial anisotropy in the low-V region suggest partial melting and horizontal melt transport. We propose that the mantle upwelling induced decompression melting in the uppermost mantle and that excess heat associated with melt transport modified the lithosphere that isostatically compensates the surface uplift at upper mantle depths (>80 km).