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In 2016, we carried out a coincidental multi-channel reflection seismic and wide-angle reflection/refraction seismic experiment along a 320-km long profile across the northeastern margin of the South China Sea (SCS). Based on these new data, we studied velocity structure of the transitional continental crust using both ray-tracing based seismic phase modeling and travel-time tomography. The velocity model shows that Mesozoic sediments have velocities of 4.3-5.3 km/s and are about 3-6 km thick in the magnetically quiet Chaoshan Depression and the attenuated transitional continental crust. This confirms that it is this thick layer of weakly magnetized Mesozoic sediments that causes the magnetic quiet zone. This Mesozoic layer pinches out seawards near the continent-ocean boundary. Two apparently isolated high-velocity anomalies are revealed in the lower crust of the continental slope. The first has velocities of 7.0-7.5 km/s and a maximum thickness of 8 km, and the second has velocities of 7.0-7.3 km/s and a maximum thickness of 3 km. We find that the discontinuity of the high-velocity zones is not due to the lack of some seismic phases or lose of a seismometer. We suggest that post-spreading magmatism caused these high-velocity zones. A third high-velocity zone, showing a distinctly large velocity gradient, is revealed near the continent-ocean boundary (COB). This indicates upper mantle upwelling and/or exhumation right at the COB, despite recent unsuccess in directly sampling these deep materials in the SCS.