Sequence analysis of high-resolution seismic profiles and sediment data from the Jeju Strait reveals that the shelf deposits form a depositional sequence consisting of a set of lowstand, transgressive, and highstand systems tracts deposited since the LGM. Six seismic units, each with different seismic facies and geometry, constitute three systems tracts. During the LGM, most of the continental shelf was exposed, resulting in sub-aerial erosion associated with paleo-channel incision, forming incised-channel fill (unit 1). The paleo-river may have supplied abundant terrigenous sediments to the study area around the paleo-river mouth. As the shelf flooded, these sediments were trapped within the paleo-estuary and formed estuarine deposits (unit 2). As transgression continued, the near-surface sediments were reworked and redistributed by shelf erosion, resulting in a thin transgressive sand sheet (unit 3) covering a large area of the shelf. Based on age dates and sea-level curves, a transgressive sand ridge (unit 4) formed during the stillstand or very slow rise period (13.7–11.5 ka BP). The Heuksan mud belt (HMB; unit 5), which is one of the prominent mud deposits located in the western part of the study area, can be divided into two subunits (5a and 5b). The lower part of the HMB (unit 5a) corresponds to shelf mud deposited during transgression. In contrast, the upper part of HMB (unit 5b) consists of recent shelf mud that was deposited during the highstand (after ∼7 cal kyr BP). The Seomjin subaqueous delta (unit 6), which consists exclusively of homogenous mud, was deposited after the sea-level highstand. Unit 6 indicates a transition from proximal to distal facies around the Seomjin River mouth. A single depositional sequence on the Jeju Strait shelf was mainly controlled by the complex interplay between bottom morphology, a varying sediment supply, and high-amplitude (∼130 m) sea-level changes, along with hydrodynamic conditions.