Studies on the coral reefs of the South China Sea (SCS) was the theme of the 6th Session of the 3rd Conference on Earth System Science (CESS) in Shanghai, 2014. This session discussed the most recent study developments on the SCS coral reefs, including coral reefs’ responses to global changes, coral reefs’ records on past climatic variations, and the activities about constructions and oilgas explorations in the coral reefs areas of the SCS. Disturbed by intensive anthropogenic activities and global climate warming, coral reefs in the SCS have declined dramatically, reflecting the up to 80% decrease of living coral cover and many areas having less than 20% of living coral cover. Geochemical data of SCS coral skeletons clearly show that since the Industry Revolution, the pollution situation of the SCS have dramatically increased and the seawater pH values have been continuously lowering, i.e. oceanic acidification. All these environmental phenomenon are further stressing the healthy development of the coral reef ecosystem in the SCS. Meanwhile, the poor coral reef ecosystems in the SCS are facing more anthropogenic disturbances such as coastal developments and engineering constructions. Obviously, the SCS coral reefs will be faced with more environmental challenges in the coming future. We therefore suggest that the policy makers should realize the extreme importance and the fragile of the coral reef ecosystems, and scientifically and with great cautions design construction project when in coral reef areas. We initiated the concept of “green engineering” for future developments in coral reef areas. Coral reefs are widely spreading in the whole SCS, and most of them developed since Miocene. Variations in coral reef structures provide good future oil-gas exploration. Because the SCS coral reefs have a long-developing history and a wide spatial distribution, they provide great potential in recording past environmental changes.