Abstract: Submarine geomorphology can reveal the topographic characteristics of seafloor, which is helpful to understand the composition, formation, evolution, and distribution of the sediment. The hydrologic elements and hydrodynamic conditions in Xuande Atoll, Xisha, Islands, South China Sea were quantitatively investigated by the combination of single beam sounding, single-channel seismology, sampling of surface sediments, and hydrodynamic measurements. Furthermore, the morphodynamic characteristics and genetic mechanism of submarine sandbanks were discussed in detail. Results show that the coral reef frame and buried corals that developed in water depth of 50～55 m and 60 m in the atoll lagoon were formed in the same period of typical landforms that formed in the 50～60 m depth during the lower sea level period of the Holocene in South China Sea. It is likely that the boundary of the submarine geomorphology developed in water depth of 50～55 m retained the paleo-lagoon reef morphology of the Early Holocene. Five types of submarine sandbanks with own morphodynamic characteristics were identified in the atoll lagoon where tidal currents at the bottom are the main modern dynamic factors that shape the submarine sandbanks. Under normal weather condition, tidal currents in the study area are strong to transport sandy sediments and shape the geomorphology of present submarine sandbanks on the previous topography formed during sea level fluctuations. The sea level fluctuations are induced by climate change, followed by topographic foundation (coral frame, reef shoreline, reef gate) and tidal currents, and are the main factors that control the development of submarine sandbanks in the study area.