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The origin of seismically-defined high-velocity lower crust (HVLC) is an important scientific issue that has attracted much debate. This study compiles 12 published wide-angle seismic velocity models from the northeastern South China Sea (SCS) to define the spatial distribution and origin of the HVLC. We have compiled the P-wave seismic velocities and interface depths of sediment, crust (including the HVLC), and mantle from each seismic profile. A pseudo-3D seismic velocity model of the northeastern SCS is then built using Kriging interpolation. Sediment thickness is 4–12 km in the Southwest Taiwan Basin and is 8–12 km at the Hengchun Ridge due to an abundant source of sediments. On a regional scale, the crust gradually thins from continental shelf and Taiwan Island toward ocean basin. Moreover, a very high crustal stretching factor (5–7) within the northeastern Southwest Taiwan Basin shows an extremely extended crust that is interpreted as a failed rift. The HVLC is spatially uneven in distribution, and seems to be divided into two parts along the paleo-Pacific subduction zone. The northwestern HVLC, located in front of the paleo-Pacific subduction zone, is distributed in a continuous stripe shape and overlapped almost with high magnetic anomalies; whereas the southeastern HVLC is distributed in the form of discrete blocks. The former one is formed by residual magmatic materials in response to the paleo-Pacific subduction, and the latter one is inferred to originate from post-rift magmatic modification. • The new pseudo-3D model shows the thickness and velocity of sediment, upper/lower crust and HVLC in spatial. • The HVLC can be divided to two types for the first time, which are bounded by the paleo-Pacific subduction zone. • Two types of HVLC are presented in continuous stripe shape and in scattered blocks pattern, respectively. • They are inferred as the Mesozoic residual magmatic material and the post-rift magmatic modification, respectively. [ABSTRACT FROM AUTHOR]