The Pearl River Canyon system is a typical canyon system on the northern continental slope of the South China Sea, which has significant implications for hydrocarbon exploration. Through swath bathymetry in the canyon area combined with different types of seismic data, we have studied the morphotectonics and controlling factors of the canyon by analyzing its morphology and sedimentary structure, as well as the main features of the continental slope around the canyon. Results show that the Pearl River Canyon can be separated into three segments with different orientations. The upper reach is NW-oriented with a shallowly incised course, whereas the middle and lower reaches, that are located mainly in the Baiyun Sag, have a broad U-shape and have experienced consistent deposition. Seventeen deeply-cut canyons have developed in the slope north of the Baiyun Sag, playing an important role in the sedimentary processes of the middle and lower reaches of the Pearl River Canyon. These canyons display both asymmetrical V-and U-shapes along their lengths. Numerous buried channels can be identified below the modern canyons with unidirectionally migrating stacking patterns, suggesting that the canyons have experienced a cyclic evolution with several cut and fill phases of varying magnitude. These long established canyons, rather than the upper reach of the Pearl River Canyon, are the main conduits for the transport of terrigenous materials to the lower slope and abyssal basin during lowstand stage, and have contributed to the formation of vertically stacked deep-water fans in the middle reach. Canyon morphology is interpreted as a result of erosive sediment flows. The Pearl River Canyon and the 17 canyons in the slope area north of the Baiyun Sag probably have developed since the Miocene. Cenozoic tectonics, sea level change and sediment supply jointly control the morphology and sedimentary structure. The middle and lower reaches of the Pearl River Canyon developed on the paleo-terrain of the Baiyun Sag, which has been a persistently rapid depositional environment, receiving most of the materials transported via the canyons.