Modern atolls have been studied systematically and thoroughly in the South China Sea. However, the knowledge of a paleo-atoll and related sedimentary system is very limited. Here we used the newly acquired high resolution 2D seismic data, and discovered three late Miocene atoll systems in the offshore Xisha Islands for the first time. We named them atoll system A, B, C, respectively. These three atoll systems, all developed on the horsts dominated by normal fault, consist mainly of atoll reefs, patch reefs, fore-reef slope deposits, and lagoons. On the basis of the interpreted sequence stratigraphic framework and the identification of fore-reef slope deposits, we suggested only the atoll system A continued to grow until Quaternary, and both of atoll system B and C had been drowned in Pliocene. In late Miocene, the atoll systems in the study area were most developed, either in magnitude or in maturity, which indicated late Miocene was the most flourishing period of reef builders, and this was in accordance with the drilling result of ODP Leg 184 in the South China Sea. Pliocene was an important reef drowning period in the study area, and both atoll systems B and C were drowned and hemipelagic deposits prevailed gradually. Quaternary was another reef drowning period in the study area, two large atoll reefs grown on the atoll system A were finally drowned, and hemipelagic deposits begun to drape and fill the palaeo-atoll systems. The growth and drowning of atolls are controlled mainly by tectonic subsidence in long term, but global eustatic can impact it in short term also.