Prior sequence stratigraphic methods mainly employed two-dimensional (2-D) stacking patterns to reconstruct stratigraphic frameworks. The future of sequence stratigraphy will pay more attention to systems-tracts scale and three-dimensional (3-D) stratigraphic variability. Using 1.2 × 104 km2 (4.63 × 103 mi2) 3-D seismic data, tied to regional 2-D seismic lines and 21 boreholes, the present study examines systems-tract scale and 3-D stratigraphic variability of the 14.8–13.8 Ma Pearl River shelf-margin to deep-water sedimentary prisms. The studied prisms were divided into four main systems tracts, namely, highstand systems tract (HST), falling-stage systems tract (FSST), lowstand systems tract (LST), and transgressive systems tract (TST). Each systems tract is represented by a given clinoformal architecture and stacking pattern: (1) clinothem sets with aggradation to progradation are HST, (2) clinothem sets with progradation to degradation (PD) are FSST, (3) clinothem sets with progradation to aggradation (PA) are LST, and (4) clinothem sets with retrogradation are TST, LST, or HST. In addition, Pearl River FSST and LST display downdip stratigraphic variabilities which are regionally manifested in at least three ways: (1) shelf-edge deltas linked downdip to basin-floor fans, (2) shelf-edge deltas linked downdip without fans, and (3) basin-floor fans linked updip that lack deltas. In along-strike orientation, the Pearl River FSST could exhibit low-angle progradation, not just PD stacking. The LST could present retrogradational stacking, not just PA stacking. Therefore, the physical position of a systems tract is reemphasized in terms of assigning a given systems tract. The concepts of three systems tracts are then revised for chronostratigraphic significance. The LST is the lowermost systems tract of a sequence, presenting a normal regression of the shoreline as its diagnostic characteristic and including contemporaneous stratigraphic units laterally. The HST is the upper systems tract of a sequence, providing a normal regression of the shoreline as its diagnostic characteristic and including contemporaneous stratigraphic units laterally. The TST is the middle systems tract of a sequence, generating a backstep of the shoreline and excluding contemporaneous onlapping units of both the LST and HST laterally. The FSST has not been revised because FSST may be a supply-independent feature.