The distribution of Holocene sediments in the Mekong River shelf area was investigated using shallow seismic and core data. The results show that the shelf depositional stratigraphy since the last glacial period can be classified into four depositional units (U1, U2, U3 and U4). The average thickness of the Holocene deposit in the nearshore area of the Mekong River estuary is approximately 20 m and decreases seaward. In addition to a thickened deposit in the palaeo-river channel, two sedimentary centres have developed, namely, the Mekong River estuary and the Cape Ca Mau area. In contrast to nearshore deposition, the Holocene sedimentation rate rapidly decreased offshore, even in the transgressive systems tract. To understand the driving mechanisms for the variation in Holocene deposition, a three-dimensional numerical model and Geographic Information System(GIS)-based model were applied to reconstruct the oceanographic and sediment transport patterns on the South Vietnam shelf. The simulation results reveal that the Mekong River shelf has undergone significant transformations since the Last Glacial Maximum (LGM). During the LGM, the coastline was situated near the shelf break, and as the sea level rose rapidly, the shoreline retreated. When the sea level reached its peak, the modern Mekong Delta emerged. Furthermore, the distribution of Holocene deposits is controlled by monsoon-influenced seasonal variations in currents, resulting in a triangular delta and narrow strip-like subaqueous clinoform. Our simulation results also show obvious erosional capacity in the offshore area, leading to an evident erosional through to the east of Cape Ca Mau and erosion of Pleistocene sediments in the shelf break area. By combining stratigraphic interpretation and oceanographic simulations, our study provides new insights into sediment transport and erosion processes mediated by ocean currents driven by East Asian monsoons.