Abstract: Gravel layers were drilled at IODP 367 Site U1499 in northern South China Sea. A variety of possible genetic mechanism for gravel layers, which are incorrect or uncertain predictions from observations in geophysical data in advance, have been proposed through the lithostratigraphic units in the cored sediment at site U1499. Using tectonostratigraphy and sediment-filling dynamics, this study restores the palaeo-geomorphology during the gravel layers sedimentation period based on a high-resolution seismic database and IODP site data from the northern margin of the South China Sea. The results indicate that the gravel layers should be deposited in proximal delta sedimentation environment along Late Eocene-Early Oligocene lacustrine basin peripheral, whose provenance is mainly from Mesozoic erosion areas of Dongsha and Liyue. The top of the gravel layers corresponds to a coincidence boundary of T70 and T60 in seismic profiles. T70 unconformity is likely directly related to the continental breakup during the initial opening of the northern South China Sea. T70 boundary age is estimated to be at 33.0–228.4 Ma and is earlier in the east than that of the west. Besides, this paper suggests that the position of ocean-continent transition zone may be near the southern edge of a series of small extensional half-grabens in the northern South China Sea rather than a geomorphic abrupt domain with a water depth of 3 000 m.