The Pearl River Mouth Basin (PRMB), located on the northern continental margin of the South China Sea, underwent a complex evolution during the Paleogene. We have focused on the Baiyun Sag in the PRMB with the goal of constructing the architecture and depositional evolution of the Eocene–Early Oligocene synrift stage to the Late Oligocene early postrift stage of basin evolution. Based on analysis of 3D seismic data complemented by well logs and cores, the Paleogene basin fills can be classified into three composite sequences bounded by regional unconformities and 14 sequences bounded by local unconformities. We identify seismic facies on the basis of different internal reflection configurations, external shapes, and contact relationships. The distribution of seismic facies and lithologies interpreted from gamma-ray curves reveal that the synrift basin fill consists mainly of fan delta deposits adjacent to the southern fault scarp, braid delta deposits on the adjacent hanging-wall blocks, and lacustrine mudstones and sublacustrine fan deposits in the center of the basin. The overlying early postrift stage is dominated by shelf and shelf-slope environments, with widespread developed southward-prograding deltas and submarine fans. Tectonics is the principal controlling factor on the development and distribution of depositional systems during the synrift stage. In contrast, sea-level changes superimposed on long-term subsidence related to thermal cooling determined the stacking patterns of sequences during the postrift stage. The results provide new insights on synrift and early postrift tectonics and sedimentation patterns along an evolving passive margin.