The southeastern Korean margin documents the processes of continental rifting and seafloor spreading that eventually led to the opening of the southern part of the East Sea (Japan Sea). Two-dimensional crustal structure of the southeastern Korean margin was computed from ocean bottom seismometer data by tomographic inversion and iterative forward modeling. The crustal structure shows the emplacement of high-velocity (>7 km/s) lower crust under the continental shelf and slope area associated with a rapid transition from rifted continental to oceanic crust. The high-velocity lower crust is interpreted as magmatic underplating formed by voluminous igneous activity during rifting. Magnetic modeling confirms its primary correlation with a prominent magnetic anomaly along the edge of the Korean Peninsula. We suggest that the rifting and subsequent seafloor spreading at the Korean margin was significantly controlled by the supply of magma in a region of hotter than normal mantle temperature.