Seismic sedimentology and sequence stratigraphy, as emerging interdisciplinary fields, demonstrate unique advantages in characterizing seismic geomorphological responses of various system tracts within the stratigraphic frameworks of rift lacustrine basins. Focusing on the Paleogene Dainan Formation in the Gaoyou Sag of the Subei Basin, eastern China, this study integrates seismic termination patterns, sedimentary cyclicity analysis, and well-to-seismic calibration to subdivide the formation into three third-order sequences containing lowstand (LST), transgressive (TST), and highstand (HST) system tracts. The distribution of five distinct sedimentary facies exhibits pronounced sub-tectonic zonations controlled by the basin’s architecture and structural evolution, with steep slope zones dominated by nearshore subaqueous fan–fan delta complexes, gentle slopes developing normal deltaic systems, and deep-semi-deep lacustrine facies with slump turbidite fans concentrated in depositional centers. Through a novel application of 90° phase adjustment, spectral decomposition, and multi-attribute fusion techniques, the relationship between seismic amplitude attributes and lithologies are established via seismic lithology calibration. Detailed sequence evolution analyses and seismic geomorphological interpretation systematically elucidate the spatio-temporal evolution of depositional systems within different system tracts in rift lacustrine basins, providing a novel methodological framework for sequence stratigraphic analysis in continental rift settings.