The Major Research Program “Deep Sea Processes and Evolution of the South China Sea”, or “The South China Sea Deep”, launched in January 2011 by the National Natural Science Foundation of China, is the first large-scale basic-research program in ocean science in the country aiming to reconstruct the life history of a marginal sea. The overall scientific objective of the program is to dissect this typical marginal sea by studying its history of evolution and its modern processes, including the following three major components: (1) Development of the deep basin: utilizing new techniques to re-measure magnetic anomaly lineations, to explore the deep tectonic features, to drill the oceanic crust, and to study volcanic seamount chains; (2) deep-water sediments: observing the modern processes to reveal the patterns of deep-water circulations and sedimentation, analyzing deep-sea sediments to recognize paleoceanographic response to basin evolution, and subsequently to bridge the modern and paleo-studies of the deep-sea processes; and (3) biogeochemical processes: using a variety of techniques including deploying submarine observation and deep-water diving device to investigate the distribution patterns and environmental impacts of deepwater seepages and sub-bottom circulation, and to reveal the role of microbes in deep-sea carbon cycling. As compared with the open ocean and other marginal seas, the South China Sea enjoys many more advantages as a marine basin for reconstructing the life history. Meanwhile, the South China Sea Deep Program provides unique opportunities in studying the evolution and variations of the sea-land interactions between the Pacific and Asia.