We present a 2‐D seismic tomographic image of the crustal structure along the OBS2012 profile, which delineates the Moho morphology and magmatic features of the northeastern South China Sea margin. The image was created by forward modeling (RayInvr) and traveltime tomographic inversion (Tomo2D). Overall, the continental crust thins seaward from ~27 km to ~21 km within the continental shelf across the Zhu I Depression and Dongsha Rise, with slight local thickening beneath the Dongsha Rise accompanying the increase in the Moho depth. The Dongsha Rise is also characterized by ~4–7 km thick high‐velocity layer (HVL) (~7.0–7.6 km/s) in the lower crust and exhibits a relatively high velocity (~5.5–6.4 km/s) in the upper crust with a velocity gradient lower than those of the Zhu I Depression and Tainan Basin. Across the continental slope and continent‐ocean transition (COT), which contain the Tainan Basin, the crust sharply thins from 20 km to 10 km seaward and a ~2–3 km thick HVL is imaged in the lower crust. We observed that volcanoes are located only within the COT, but none exist in the continental shelf; the Dongsha Rise exhibits a high magnetic anomaly zone and different geochemical characteristics from the COT. Based on those observations, we conclude that the HVL underlying the COT is probably extension related resulting from the decompression melting in the Cenozoic, whereas the HVL beneath the Dongsha Rise is probably arc related and associated with the subduction of the paleo‐Pacific plate. These findings are inconsistent with those of some previous studies.