High-resolution 2D and 3D seismic data are used to investigate the morphology, internal architecture and origin of widespread seafloor undulations in the eastern area of a submarine canyon system, northern South China Sea. The seafloor undulations reveal similar seafloor morphologies, and three different types (Types A, B and C) can be classified based on their relative locations and internal seismic characters. Types A and B are observed in the canyon areas, whereas Type C occurs in the canyon heads. Seismic reflections within Types A and C are continuous and have an upslope migrating trend, while Type B seafloor undulations are separated by listric faults. Our analysis reveals the origins of these three different types of seafloor undulations. Type A seafloor undulations are sediment waves formed by turbidity currents flowing through the submarine canyons. Gravity-driven submarine creep resulted in the formation of Type B seafloor undulations. Type C undulations are sediment waves generated by internal waves interacting with the continental slope. Our results provide information about the origin of widespread seafloor undulations in other submarine canyon systems. It is also of great significance to future risk assessments, as the study area now is one of the most active regions for hydrocarbon exploration in SE Asia.