An E-W oriented OBS2015-2 wide-angle refraction profile was shot in the northeastern South China Sea (SCS) between refraction profiles T1 and T2 in order to better understand the variability of the crustal composition and the role of specific tectonic features. P-wave velocity models established from forward and inversion modeling imaged a 12 to 15 km-thick thinned continental crust and a high velocity layer (HVL) in the lower crust which is interpreted as magmatic underplating. Profile OBS2015-2 cut across the Taiwan transfer zone (TTZ), which separates two consecutive rifted segments of different orientations in the northeastern SCS. The TTZ is a well-defined upper crustal feature characterized by a HVL with different thickness on both sides. We have defined the southward limit of the thinned continental domain with the typical oceanic domain as a continent-ocean boundary (COB). The COB between the drilling area of IODP legs 367–368 to the Manila trench is characterized by a sharp contrast between the low amplitude, irregular shape magnetic anomalies and the high amplitude, elongated shape magnetic anomalies, which are associated with the thinned continental domain and the oceanic domain, respectively. We further extend the COB into the 400 to 500 km wide unfolded Manila slab located east of the Manila trench by using mid-slab dVp tomographic velocities to define the boundary between subducted oceanic and thinned continental crust. The location of the reconstructed northeast SCS COB appears to step northwards toward Taiwan across a 400 km N-S segment, providing new constraints on SCS geodynamics at the end of spreading and its later tectonic evolution.