Over the last two years, Chinese scientists from the both sides of the Taiwan Strait and from overseas, met several times to discuss the direction of deep-sea research in China. All agreed that the South China Sea should be the first priority, and a preliminary sketch of research program of the “The South China Sea Deep” was drafted. The overarching goal of the proposed program is to unveil “the life of a marginal sea”, from three major perspectives: (1) evolution of the oceanic crust in the deep basin, which will be revealed by validating the magnetic anomalies in the South China Sea using new techniques, implementing deep-water drilling of the oceanic crust, and systematically investigating the volcanic mountain chains in the basin; (2) deep-sea sedimentation, including observation of the modern deep-water currents and benthic sedimentation, and reconstruction of sediment response to the evolution of the marginal basin; and (3) biogeochemical processes to be approached by exploring the dynamics and consequences of subsurface fluid circulation, and by evaluating the microbial contribution to the deep-sea carbon cycling. Research breakthroughs are expected in the South China Sea on the basis of nation-wide cooperation with a combined effort by the scientific and engineering communities.