Submarine channel systems transport vast amounts of terrestrial sediment into the deep sea via turbidity currents, however, there is a paucity of research detailing their dynamics, especially regarding the issue of how flows transport sediment and deposit at channel bends and channel junctions. From the analysis of core data, a high-resolution 3D seismic dataset, and local topography, a 3D numerical model is used to simulate the evolution of turbidity currents containing multiple size classes of sediments in the Late Miocene submarine channels in the Yinggehai Basin, northwestern South China Sea. The model solves the Reynolds-averaged Navier–Stokes (RANS) equations, the mass conservation equation, and the Exner equation for bed evolution caused by sediment entrainment and deposition. The results for the tendency of the total volumetric concentration of sediment in the turbidity current and bed thickness distribution reasonably match the infilled thickness of the channel interpreted from seismic data. The turbidity current in submarine channels is limited by the sloping topography and the channel geometry. Geochemical results show that, during the Late Miocene, sediments were derived from mixed sources. The simulation result accurately reveals the scope and magnitude of sediment contributions from each provenance. The confluence zone of the two channels (W and E) receives coarse-grained thick-bedded sediments via E channel flow transport showing a homogeneous distribution, a good hydrocarbon reservoir. This study improves our understanding of the processes of turbidity currents and their depositional characteristics within submarine channels, the reconstruction of their depositional environment, flow structures, spatial partitioning of sediment, and reservoir distributions within sinuous channels.