Investigating the deposition evolution and stratal stacking patterns in continental rift basins is critical not only to better understand the mechanism of basin fills but also to reveal the enrichment regularity of hydrocarbon reservoirs. The Pearl River Mouth Basin (PRMB) is a petroliferous continental rift basin located in the northern continental shelf of the South China Sea. In this study, the depositional evolution process and stacking pattern of the Zhu III Depression, western PRMB were studied through the integration of 3D seismic data, core data, and well logs. Five types of depositional systems formed from the Eocene to the Miocene, including the fan delta, meandering river delta, tidal flat, lacustrine system, and neritic shelf system. The representative depositional systems changed from the proximal fan delta and lacustrine system in the Eocene−early Oligocene, to the tidal flat and fan delta in the late Oligocene, and then the neritic shelf system in the Miocene. The statal stacking pattern varied in time and space with a total of six types of slope break belts developed. The diversity of sequence architecture results from the comprehensive effect of tectonic activities, sediment supply, sea/lake level changes, and geomorphic conditions. In addition, our results suggest that the types of traps are closely associated with stratal stacking patterns. Structural traps were developed in the regions of tectonic slope breaks, whereas lithological traps occurred within sedimentary slope breaks. This study highlights the diversity and complexity of sequence architecture in the continental rift basin, and the proposed hydrocarbon distribution patterns are applicable to reservoir prediction in the PRMB and the other continental rift basins.