The structural evolution and topography controlled by thrust faults in continental slope of Niger Delta Basin deserve further study. Based on 3D seismic data in one deep water zone, three super sequence boundaries are identified, by which the Cenozoic is divided into three super sequences(SSQ1, SSQ2, SSQ3), and three detachment levels are analyzed. As about the SSQ3, it is divided into three sequences from bottom to top, representing three stages controlled by thrust fault, mud-diapir, and sedimentation respectively. In the first stage, thrust faults developed along detachment level in different depth under the control of gravity slide, and due to the translocation difference, tear fault perpendicular to the strike of thrust faults developed in transfer zone. Along the tear fault, mud-diapir fold formed under the control of overpressure mud. The gravity flow transported along the structural lows in the hanging walls of thrust faults, thus lithologic traps concentrated in minibasins. In the second stage, huge detachment fold formed due to the concentrating of overpressure mud at the core of thrust-related fold and tear-related fold under the control of load difference, in which the deformation of mud is confined by the detachment levels. The gravity flow and lithologic traps developed along the structural lows on both sides of the mud-diapir anticline. In the third stage, the structural activity weakened obviously, and the topography tended to be flat under the control of sedimentation.