Coring/logging data and physical property measurements from International Ocean Discovery Program Expedition 349 are integrated with, and correlated to, reflection seismic data to map seismic sequence boundaries and facies of the central basin and neighboring regions of the South China Sea. First‐order sequence boundaries are interpreted, which are Oligocene/Miocene, middle Miocene/late Miocene, Miocene/Pliocene, and Pliocene/Pleistocene boundaries. A characteristic early Pleistocene strong reflector is also identified, which marks the top of extensive carbonate‐rich deposition in the southern East and Southwest Subbasins. The fossil spreading ridge and the boundary between the East and Southwest Subbasins acted as major sedimentary barriers, across which seismic facies changes sharply and cannot be easily correlated. The sharp seismic facies change along the Miocene‐Pliocene boundary indicates that a dramatic regional tectonostratigraphic event occurred at about 5 Ma, coeval with the onsets of uplift of Taiwan and accelerated subsidence and transgression in the northern margin. The depocenter or the area of the highest sedimentation rate switched from the northern East Subbasin during the Miocene to the Southwest Subbasin and the area close to the fossil ridge in the southern East Subbasin in the Pleistocene. The most active faulting and vertical uplifting now occur in the southern East Subbasin, caused most likely by the active and fastest subduction/obduction in the southern segment of the Manila Trench and the collision between the northeast Palawan and the Luzon arc. Timing of magmatic intrusions and seamounts constrained by seismic stratigraphy in the central basin varies and does not show temporal pulsing in their activities. Key Points First core‐log‐seismic correlation in the central South China Sea basin The fossil ridge and subbasin boundary acted as major sedimentary barriers Seismic facies and migration of depocenter responded to tectonic events