Abstract: Notable differences in the structural characteristics and evolution of three adjacent sub-sags, i.e., the Wenchang sub-sags A, B, and C, on the downthrown side of the Zhu III South Fault in the Wenchang Sag, are significant as they affect the formation and distribution of the oil and gas in these three sub-sags. However, the differences in their tectonic evolutions and formation mechanisms have not yet been adequately explained. In this paper, stress analysis, equilibrium profiles, and paleogeomorphic restoration, are used to investigate the dynamic settings, formation mechanisms, and influencing factors of the structural deformation related to the formation of the Wenchang Sag based on interpretation of seismic data. The results of the stress analysis suggest clockwise deflection of the regional tensile stress direction from a WNW-ESE trend during the Early Paleocene to NW-SE and NNW-SSE trends during the Eocene, to a nearly N–S trend during the Oligocene, and finally to a NNE-SSW trend during the Miocene. This clockwise rotation of the regional tensile stress direction led to the formation of a dextral strike-slip stress component parallel to the NE-trending Zhu III South Fault. This strike-slip stress component formed a releasing bend in sub-sag A, and may be associated with the continuous subsidence of a thick sedimentary layer in sub-sag A. It also created a restraining bend in sub-sag B, which underwent multiple structural inversions during its extension and subsidence and has a relatively small sedimentary thickness. The double restraining bend in sub-sag C is considered to have been strongly uplifted and eroded in response to this strike-slip stress component. Four obvious structural inversions in sub-sag B are identified in this paper. These structural inversions correspond to the last four regional tectonic movements. This interpretation suggests that the formation of the structural inversions was likely related to the strong tensile stress and the small intersection angle between the direction of the regional tensile stress and the pre-existing boundary fault. The rotation of the tensile stress direction was responsible for the strike-slip movement on the pre-existing boundary fault and the formation of the releasing bend and restraining bend, which controlled the structural evolutions of the sub-sags. This reasonably explains the differential tectonic evolution of these three sub-sags in the Wenchang Sag, and provides a crucial idea for structural analysis of similar basins.