Multichannel seismic reflection profiles and well data were analyzed to unravel the origin and depositional history of stacked cut-and-fill structures (CF) in the southwestern margin of the Ulleung Basin, East Sea. The CFs in a syn-compressional megasequence are characterized by discontinuous, low-amplitude, chaotic, and transparent seismic reflections. They display both U-shaped and V-shaped morphologies along their lengths. The CFs are thickest and widest at the shelf edge and taper both landward and basinward. Based on the stratigraphic position, the CFs are found in three depositional sequences (DS8–DS10). Thirty CFs have been identified that range from 0.5 to 8.8 km in width and 58 to 453 m in thickness (assuming a 2000 m/s seismic velocity of the sediments). The larger and numerous CFs occurred in the middle depositional sequence. Seismic characteristics, spatial distribution, hundred-meter-scale incisions, and high gamma-ray responses indicate that the CFs were caused by submarine canyons. During the period of DS8, small CFs were formed locally on the shelf margin, and were little influenced by the deformation of the thrust-fold (Dolgorae Thrust Belt). Extensive and numerous CFs in DS9 developed in the oversteepened shelf margin, where uplift of both the thrust-fold and anticline (Gorae V structure) occurred simultaneously, and where a large volume of sediment was supplied. During the period of DS10, a general decreasing pattern in the occurrence and dimensions of the CFs resulted from waning tectonic activity of the thrust-fold that reduced sediment supply. Consequently, this study suggests that variation in contractional tectonic activity and sediment supply, associated with the back-arc closure of the East Sea, mainly controlled the evolution of the CFs rather than eustasy.