In this study, we use 3D seismic, well‐log, and core data to investigate the sequence stratigraphy and facies associations of the Paleogene in the Nanpu Sag, Bohai Bay Basin, East China. Three second‐order sequences—SQEs3‐SQEs2, SQEs1, and SQEd—and 12 third‐order sequences are identified. Fan‐delta, braid‐delta, sublacustrine fan, and lacustrine systems are identified. Four types of tectonic‐induced sequence models are distinguished, which consist of fault‐cliff type, fault‐slope type, axial ramp type, and multiple fault‐terrace type. Sequence architecture of third‐order sequences is dominated by thin lowstand systems tracts with thick transgressive systems tracts (TST) and highstand systems tracts (HST). High‐resolution sediment‐partition pattern analysis shows that a large volume of sediments can be delivered into prodelta/deep‐lacustrine environments during transgressive periods and lake‐level highstand. This study also shows that sand/strata ratios in fan‐delta/braid‐delta front of systems tracts scale have a negative correlation with the subsidence rate, which is demonstrated by the finding that higher subsidence rates correspond to lower sand/strata ratios. This result suggests that subsidence rate has a significant influence on high‐frequency sequences. The occurrence of the high volume of sand‐rich deposits developed in TST and HST and relatively high sand/strata ratios within these sequence units reveal that TST and HST could also have a high hydrocarbon potential. The strongly asymmetrical accommodation generated by an early rapid tectonic subsidence and late tectonic quiescence results in sequence architecture variations between passive‐margin basins and rift basins. Different subsidence rates among different structural belts result in sequence architecture variations within different sequence models.