Abstract: The OBS2006-3 profile located in the northeastern South China Sea (SCS), as an integrated endeavor of geophysical research, passes through the Dongsha Islands and the Chaoshan Depression, and ends at the margin of the ocean basin. Density modeling remains the pivotal part of the research. Based on the model, combined with the geological and geophysical data available, it is revealed that:(1) A Mesozoic subduction zone might occur in the sea area around the Dongsha Islands, which might be the same as the East Asia subduction system. The Dongsha fault is probably the paleo-suture zone, and the Chaoshan depression might be the Mesozoic fore-arc basin, and the Dongsha-Peikang uplift might be a paleo-volcanic arc. (2) The thickest Mesozoic in the Chaoshan depression is around~9 km with oil and gas potential. There may be magmatic intrusions and/or metamorphism to certain extent.