Abstract: The river channel system is an important passage for erosion and sediment transport, which controls the overall transport and distribution pattern of sand bodies in the source-sink system of the continental margin, which indicates effectively the tectonic subsidence, sediment supply, climate change, and sea level change of the ancient sedimentary environment. Based on the high-resolution 3D seismic data, well logging and coring data, the types and distributions of the fluvial system in the Early-Mid Miocene of the Zhu I Depression in the ancient Pearl River Delta, northern South China Sea were studied in combination of the classification of the sequence stratigraphy and comprehensive seismic-sedimentary analysis. Furthermore, representative sequences were used to analyze the transition mechanism of fluvial types controlled by sea-level change. Abnormal incisions in large numbers were identified from the high-resolution seismic profiles of the study area, which can be interpreted as confluence scour in a braided channel. The typical characteristics are as follows: (1) showing local increase of cutting depth; (2) being approximately circular or elliptical in plan view; and (3) the interior being filled with sand. Although the confluence scour structure is easily confused with the incised valley in seismic profile, it is quite different in sedimentary characteristics and genesis. Therefore, the identification of confluence scour could help avoid wrong interpretation of sequence boundary, and they are filled with sediments carried by later fluvial channels, which is easy to form a new type of potential lithologic trap under the cover of the later transgressive mudstone. The confluence scours facilitated the access to the reservoirs and connected the stacked fluvial sandstones, which effectively enhanced the internal connectivity of sandstone reservoirs.