Abstract: In addition to the growth of hermatypic corals, the accumulation of coral sand is also a significant factor in shaping atoll topography. The grain size of 17 surface sediment samples collected from the shallow waters of the Zhongsha Great Atoll in the South China Sea were analyzed, the seabed-based current was observed at five stations, and the sediment transport trends were also analyzed to understand the erosional and depositional status of the atoll, providing a theoretical basis for the preservation of atoll topography. Results indicate that the sediments consist of three types: gravelly sand, sandy gravel, and sand-bearing gravel, and they were transported via mainly rolling and saltation. In addition, the hydrodynamic environment, the Great Atoll region was divided into three sedimentary environment zones. Zone A (sandy transition zone): Located on the eastern and northwestern sides of the outer ring of the Great Atoll, dominated by gravelly sand, representing a high-energy reef flat sedimentary environment. Zone B (gravel accumulation zone): Stretching in NW–SE along the Luba Ansha–Manbu Ansha–Haijiu Ansha in the central part of the Great Atoll, composed of chiefly sandy gravels. This zone serves as the primary source of coarse-grained materials for the atoll, indicating rapid, near-source, mixed accumulation processes. Zone C (sand-loss zone): Located at Bohu Ansha in the southwestern part of the Great Atoll, composed of mainly sand-bearing gravel. This zone is characterized by sandy sedimentation and sorting under the influence of strong currents. While hydrodynamics in Zones A and B could transport only a small amount of fine sediments, the maximum current velocity in Zone C could exceed the threshold of sediment motion, resulting in the loss of coral sand. In the future, local monitoring shall be strengthened, and appropriate measures shall be taken to prevent sediment loss.