In addition to the continental slope and basin floor, gravity flow deposition on the shelf is increasingly attracting attention. In order to explore the environmental conditions and sedimentary rules of large-scale gravity flow deposition in shelf sea, paleogeomorphology restoration and identification, distribution and evolution of sediment gravity flow units in the upper Miocene Yinggehai Basin are studied by using 3D seismic, borehole and seismic inversion data. Two third-order sequences (SQhl2 and SQhl1) are identified, and the planar distribution of strata and turbidite deposition are controlled by different styles of slope breaks. In SQhl2, turbidite systems of subaqueous shelf fans and channels are identified. The shelf fans can be classified into early lowstand fans, late lowstand fans and highstand fans. In the early lowstand systems tract, the fans are the largest in scale (more than 700 km2), distributed in the subsidence center, and controlled by the basinward flexure slope break zone formed by fault activity. The shelf channels are classified into slope-parallel channels and slope-perpendicular channels according to the relationship between the strike of channels and the basin axis. The formation of the slope-perpendicular channels was controlled by large-scale global sea-level falls that happened 10.5 Ma ago. The formation of the slope-parallel channel was controlled by the flexure slope-break zone caused by activity of multiple groups of en-echelon faults. This study suggests that the development of large-scale turbidite systems in shelf sea was controlled by semi-enclosed geomorphology, fault activity and high sediment supply under sea-level falls. The semi-enclosed bay topography and local subsidence centers in the basin ensured a relatively isolated source-to-sink system, and allowed a large number of terrestrial sediments to converge intrabasin instead of being transported further to extrabasin. Fault activity formed structural slope-break zone and provided a “slope system” that facilitated the triggering of gravity flows on the shelf. Sharp increase of sediment supply under sea level falls contributed to the development of large-scale shelf turbidite systems. The study of large-scale turbidite system in shelf sea is of great significance for deepening the sedimentary law of gravity flow under different sedimentary backgrounds and opening up a new field for oil and gas exploration.