Carbonate platforms form informative archives for paleoclimates and their internal structures can also hold crucial information about the tectonic history and carbonate evolution of the ocean basins. The Zhongsha atoll (Macclesfield Bank) forms the largest atoll system in the South China Sea with a surface area of 23500 km2. However, the internal structure and evolution of this atoll system is completely unknown. 2D multichannel seismic reflection data were acquired in 2017 over the Zhongsha atoll in the South China Sea to unravel the stratigraphy, geomorphology, depositional processes, and seismic facies of one of the world's largest atoll for the first time. This Neogene carbonate platform comprises more than 1 km thick carbonate sequence and overlies a metamorphic basement. The southeastern part of the atoll comprises a fault-controlled graben system, which was formed during the Cenozoic rifting stage of the South China Sea. Most of the faults trend NE-SW and E-W and terminate at or slightly above the top of Middle Miocene strata. Atolls and abundant organic reefs initiated on the positive relief and closely mimicked the underlying topography during the Early Miocene. Shallow-water carbonates continued growing through Middle Miocene to present times. Regional uplift led to subaerial exposure, termination of platform growth and karstification during the Miocene. We also reveal a number of fluid-flow features such as vertical sub-bottom venting features (chimneys and pipes), chaotic reflection zones, which provide the first evidence of active fluid venting in the area of Zhongsha atoll. The Neogene sedimentation history of Zhongsha atoll further provide an important paleoenvironmental context for future scientific drilling to better constrain the evolution of Asia Monsoon.