The third member of Shahejie Formation (Sha-3 member; 42–38Ma of Eocene) in the Bozhong Depression, offshore Bohai Bay Basin was subject to multiple post-depositional modifications. The present structural framework of the Bozhong Depression, which is characterized by sags alternating with uplifts, does not reflect its original sedimentary pattern. Previous studies have not discussed the post-depositional modification of this succession, including the sedimentary pattern variations and the depositional geodynamic setting. This work determined the characteristics of the post-depositional modification and original sedimentary pattern of the Bozhong Depression through analysis of seismic data, well-log data and fission-track ages. The results demonstrate that the Shijiutuo rise, a major structural feature of the current basin, did not exist during the major depositional stage of the Sha-3 member, when the Qinnan sag was largely connected to the Bozhong sag to form a single contiguous deposition area within the basin. By contrast, the Shaleitian and Chengbei rises, located in the western part of the Bozhong Depression, have existed before the depositional period of the Eocene Sha-3 member; these features were manifested as syn-depositional tilted fault blocks, the uplifted footwall blocks of which provided sediments for the neighboring Shanan and Chengbei sags. The western part of the Bonan low rise, located in the southern part of the Bozhong Depression, did not experience uplifting during the depositional phase of the Eocene Sha-3 member. The Huanghekou sag was connected with the Bozhong sag in the western part of the Bozhong Depression. The original sedimentary boundary of the southern Miaoxi sag possibly extended eastward about 10 km and connected with the Bozhong sag at its northern part. The present-day Bodong low rise, which is bounded by the Tan–Lu fault zone, also formed after the depositional period of Eocene Sha-3 member. It is thus concluded that the Bozhong Depression formed a connected large-scale sub-basin during the depositional stage of the Eocene Sha-3 member. Several neighboring sags that are now separated by rises, including the Qinnan, Shanan, Chengbei, Huanghekou, Miaoxi and Bodong sags, formed a single contiguous depositional area during the Eocene. The significant differences between the present and original basin patter and framework provide valuable information for better understanding the history of basin inversion and its impact on related hydrocarbon-system evolution.