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The land-sea transition zone in the northern South China Sea (SCS) records important information from the continental rifting to the seafloor spreading. The crustal structure is the key to explore the deep tectonic environment and the evolution of the SCS. In 2015, the onshore-offshore 3D deep seismic experiment was carried out on the Pearl River Estuary (PRE). Explosions and air guns were used as sources on land and at sea respectively in this experiment.Onshore seismic stations and Ocean Bottom Seismographs (OBSs) synchronously recorded the seismic signals. We focus on an onshore-offshore seismic profile (L2, SE-trending) along the eastern side of the PRE. By modelling the seismic travel times, we constructed a P-wave velocity model along the profile. The model shows that the sediment on land is thin and has seismic velocities of 4.5–5.5 km/s. In contrast, thickness of the offshore sediment gradually increases to more than 4.0 km, and the velocities vary between 2.0 km/s and 4.5 km/s. The onshore and offshore crustal velocities are 5.8–6.8 km/s and 5.5–6.8 km/s, respectively. At depth between 15 km and 20 km, a low-velocity layer (LVL; only 5.9 km/s) is detected, pinching out under the Littoral Fault Zone (LFZ). The LVL has probably accommodated the crustal extension beneath the land area, resulting in low extent of the crustal thinning. A slightly uplifted Moho exists beneath the Dongguan fault depression zone, representing a place where hot mantle materials ascend. Localized thickening of the sediments and rapid thinning of the crust characterize the LFZ, and it can be regarded as a tectonic boundary between the South China (SC) with normal continental crust and the northern SCS margin with extended continental crust. [ABSTRACT FROM AUTHOR]