Previous sequence stratigraphy research has mainly focused on two-dimensional seismic interpretation in the dipping direction, while variations in sequence architecture in the vertical provenance direction are the focus and difficulty of current research. This study considers the Late Pleistocene (0.125 Ma to the present) shelf-margin stratigraphic successions of the Qiongdongnan Basin as a typical example. The internal structure and combination characteristics of the system tract units were established and identified according to typical stratal termination, stratal stacking patterns, and shelf-edge migration trajectories. The systems tracts in the studied sequence were classified from bottom to top, including the Lowstand Systems Tract (LST), Transgressive Systems Tract (TST), Highstand Systems Tract (HST), and Falling-Stage Systems Tract (FSST). The surface of Within Systems Tract Surface (WSTS) divides the FSST into early and late phases. The WSTS interface is the transitional surface for the positive-to-negative angle of the migration trajectory of the shelf edge and for the stratal stacking transition from progradation to degradation. Stabilized and collapsed shelf-edge sequence architectures developed during the Upper Pleistocene in the western part of the eastern Qiongdongnan Basin. With the change in relative sea level, the stabilized shelf edge mainly developed multi-phase shelf-margin clinoforms and deep-water fan deposits, whereas the collapsed shelf edge mainly developed large-scale canyons and mass transport deposits. In response to the short sea-level rise but prominent falling cycle, the late Pleistocene shelf-edge sequences were composed of thin or undeveloped LST and TST units and a thick FSST unit, whereas the active faults in the outer shelf locations increased the proportion of the HST unit in the sequences. The pre-existing slope-break geomorphology, fault activities, and asymmetric sea-level fluctuations coevally led to the diverse sequence architectures in the study area. The quantitative exploration of high-frequency sequence stratigraphic driving mechanisms is a future development trend in Pleistocene stratigraphy, and this study provides a potential reference for the standardization of 3D sequence stratigraphic investigations.