Research into the contourite deposits in the Upper Meishan Formation of the southern Qiongdongnan Basin in South China Sea is weak; their characteristics, distribution and original geological conditions are not clear. Using geological and geophysical methods including seismic and drilling data, based on seismic reflection characteristics, geometrical configuration description, and wave impedance inversion, two types of contourite deposits are recognized. Contourite deposits have blurred boundaries between each deposit and disordered internal seismic reflections; They are mound-shaped only in transverse section, and banded in the longitudinal direction. Type I contourite deposits are conical, with medium-high amplitude, low-continuity, low-frequency mound-shaped seismic facies, and subparallel-chaotic reflections internally. These deposits are conical with sharp tops, the canal between mounds is V-shaped and deep. The western wing is gentle and the eastern wing is steep, with the slope toe mostly between 10° and 20°, and width height ratio about 1–2. Type II contourite deposits are flat, exhibiting medium-amplitude, medium-continuity, low-frequency mound-shaped seismic facies, with subparallel weak reflections internally. Their mounds are flat with gently arced tops, with shallow canals between. The slope toe is between 5° and 10°, with a width height ratio of about 2–5. The wave impedance value of these contourite deposits is 4.6 kg/m3×m/s to 6.8 kg/m3×m/s, about 5.8 kg/m3×m/s on average, which is presumed to represent marly-calcareous clastic sediments. The contourite deposits mainly develop beneath the slope break at the margin of the fault-controlled platform in the Southern Uplift zone of the basin. In plane view, they are distributed approaching a west-to-east direction, and in section, lie in low-lying areas near the faults at fault-controlled terraces of the Southern Uplift zone, with a paleo-current direction nearly west-to-east. The paleotectonic setting of the gentle monoclinic platform was favorable for the development of such contourite deposits. The intensification of the Mid-Miocene deepest bottom current gave rise to the contourite-forming currents around the Southern Uplift zone in the northern South China Sea, which flow from Hainan Island to the Xisha Trough in a nearly west-to-east direction leading to the contourite deposits developing in the late Mid-Miocene transgressive environment, with multiple slow sea-level fall cycles.