Submarine canyons are key elements in source-to-sink systems that are commonly developed along continental margins. They act as major conduits transferring sediment and pollutants from continental shelves to deep-water basins, and control the general morphology and evolution of continental margins. This work uses multibeam bathymetric and high-resolution (two- and three-dimensional) seismic data to investigate the main factors controlling the morphology of the Shenhu Canyon System in the northern South China Sea, as well as its detailed morphological character. The Shenhu Canyon System consists of nineteen (19) submarine canyons whose morphologies vary from southwest to northeast along the continental slope. Canyons (C1–C10) in the southwest show greater incision depths, and steeper thalwegs and walls, when compared to their counterparts to the northeast (C11–C17). The southwest canyons are located close to the shelf edge, where the upper continental slope is relatively steep and multiple landslides are imaged. We show that the thalwegs and walls of the southwest canyons were more actively eroded by sediment flows, with respect to the northeast canyons, making them deeper and steeper. Hence, submarine canyons in the southwest, with a more linear geometry, are now directly connected to the Pearl River Canyon. In parallel, seafloor fault scarps act as barriers for sediment transported to the heads of the northeast canyons. This research highlights how sediment supply, sediment pathways, and seafloor scarps can influence submarine canyon morphology along continental slopes. It contributes to a better understanding of the factors controlling canyon morphology worldwide.