The continental shelf strata provide information regarding sea-level fluctuation and climate changes in the Quaternary period. A 5831.47-km-long high-resolution seismic profile and borehole core (YS01) were acquired to reconstruct the evolutionary history of the strata in South Yellow Sea (SYS) during the late Pleistocene. The strata recorded three transgression events (HI, HII, and HIII) and three stages of paleochannel development (LI, LII, and LIII). Based on the distribution, thickness, and volume of the strata formed in the three transgressions, we concluded that the scale of the three transgressions during the late Pleistocene was HIII, HI, and HII, in descending order. In addition, our data show that the Yellow River extended to the Yellow Sea Trough during the last glacial maximum. The influence of the tectonic framework on sedimentation in the SYS was completely concealed by sea-level changes and sediment supply in the late Pleistocene (~Marine Isotope Stage 5). Since then, the accommodation space, a crucial prerequisite for sedimentation, has been controlled solely by sea-level changes in the SYS. Furthermore, two “source to sink” models of the neritic shelf in the marine and terrestrial environments were established, including high sea-level and shelf-exposure models.