Deep crustal structure in the northeast South China Sea (SCS) contains important information of the rifting process of the SCS. A wide-angle NW-SE trending ocean bottom seismometer profiling (DP13) was carried out across the Dongsha Rise (DSR) and Southwest Taiwan Basin (SWTB). The P-wave velocity structure model has been established by using ray-tracing and forward travel-time modeling method (RayInvr). The velocity model reveals that the sedimentary strata have velocities of 1.6~4.6 km/s and are about 0.5~3.8 km in thickness, with a non-uniform distribution laterally. The sedimentary basement is rugged and rough. The depth of the Moho interface decreases sharply from 25.5 km within the continental shelf to 13 km beneath the slope, and then increases to 16 km in the distal margin. The continental crust thins from ~25 to ~21 km within the continental shelf across DSR, and the crust in the distal margin is 10~13 km in thickness. The results show that crustal stretching factor are estimated to be 1.3~1.5 and 2.6~3.1 respectively, indicating slight and moderate crustal thinning. Across the continental slope, which contains SWTB, the crust sharply thins from 17 to 7~8 km, corresponding stretching factors > 4.6, meaning that the crust has been hyperextended. Overall, the crustal thickness is non-monotonic seaward and the crustal stretching behaves obvious variability in space. Two relatively isolated high-velocity anomalies were revealed in the lower crust beneath the continental shelf-upper slope and lower slope. The first has velocities of 7.0~7.5 km/s and thicknesses of 3~5 km, and the second has velocities of 7.0~7.3 km/s and a maximum thickness of 3 km. The former, which is located in the front of the Paleo-Pacific subduction zone and overlapped almost with high magnetic anomalies in northeast of the SCS, is formed by residual magmatic materials associated with the subduction and rollback of the Paleo-Pacific plate during Mesozoic, whereas the latter is due to the post-rift magmatic underplating/intrusions.