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Objective The Beikang Basin, located in the southern South China Sea, is a significant area for offshore oil and gas exploration in China. Previous studies in this region have primarily focused on the Palaeogene source rock and the Middle Miocene carbonate reservoirs, neglecting the investigation of deep-water sediments since the Late Miocene. Methods Therefore, this study aims to explore the spatiotemporal distribution, characteristics, and controlling factors of deep-water sediments in the Beikang Basin since the Late Miocene, utilizing 2D seismic data. Results Three types of sedimentary deposits have been identified in the Beikang Basin since the Late Miocene: draping strates, mass-transport deposits (MTDs), and turbidites. Turbidites can be further classified into confined turbidites and delta-front ones. The study reveals that the draping state is predominantly developed in the forebulge tectonic regions of the Beikang Basin, with a decreasing thickness from South to North. MTDs, on the other hand, are mainly distributed in the Backbulge zone, with a thickness that decreases from Southwest to Northeast. The findings indicate that the development and distribution of sediments in the Beikang Basin are influenced by various factors, including sedimentary supply, geomorphic features, tectonic activity, and eustatic sea level changes. The location and thickness of deep-water sediments are primarily controlled by the supply of materials. Additionally, the distribution range of gravity flow deposits and draping states is influenced by the topography of the area. Conclusion These results provide a theoretical foundation for understanding the development and controlling factors of deep-water sediments in the Beikang Basin.