AbstractSequence architectures along the margins of rift basins are still poorly documented compared to passive continental margin settings. The Eocene Shahejie Formation on the rift margin of the Dongying Depression records a complex sequence stratigraphic distribution of conglomerate, sandy conglomerate, sandstone and mudstone. These facies have been mainly attributed to fan delta and marginal subaqueous fan depositional settings that developed during segmented fault activity along the rift margin. We utilize three‐dimensional (3D) seismic data, conventional cores, and wireline log data to dissect the overall wedge‐shaped upper sub‐member strata of the Shahejie Formation's fourth member. The study interval is a third‐order sequence formed between 45.4 and 42.5 Ma and contains a lowstand–transgressive systems tract (LST–TST) and a highstand systems tract–falling‐stage systems tract (HST–FSST). We found that the LST–TST developed several huge amalgamated depocenters along the Chennan border fault; whereas, these depocenters gradually diminished or even disappeared during the HST–FSST period, illustrating less significant control by the border fault. Through calculations of strata growth rates, we confirmed that the segmented activity of the border fault influences the stratigraphic distribution and facies evolution during these two periods. Specifically, deep‐water depositional systems, represented by marginal subaqueous fans were widely developed in the LST–TST period and were influenced by overall strong tectonic activity, including retrogradational (R) and aggradational (A) patterns. However, the aggradational to progradational (AP) deltas and progradational to degradational (PD) deltas dominated the generally muted tectonic activity setting during the HST–FSST. Additionally, influenced by localized segmented fault activity, these systems tracts exhibit incomplete vertical development, resulting in spatial variability in stratigraphic stacking patterns.