The reactivation of pre-existing faults exerts a profound influence on the formation of rift basins and the deformation behaviors within their interiors, however, the specific modes of activation and underlying mechanisms remain unclear. The Enping-17 Sag, located in the tectonically active Pearl River Mouth Basin of the South China Sea, exhibits complex fault geometries and rapid subsidence since the Neogene. Its distinctive coexistence and differential reactivation of inherited fault sets make it an ideal location to investigate structural inheritance and basin evolution. In this study, high-resolution three-dimensional seismic data were employed in conjunction with seismic interpretation, dynamic analysis, and kinematic modeling to investigate the geometric attributes, activity, and genesis of sag-controlling faults. The results reveal that the boundary faults of Enping-17 Sag exhibit significant variations in strike, transitioning from a near N–S-trending in its southern segment to an ENE-trending in its northern segment. In cross-sectional profiles, the northern segment exhibits a ramp-flat geometry and records four distinct depositional periods (Early Wenchang, 49–43 Ma; Late Wenchang, 43–39 Ma; Enping, 39–32 Ma; Zhuhai, 32–23.8 Ma), whereas the southern segment displays a listric geometry, recording two prominent depositional periods (Early Wenchang, 49–43 Ma; Late Wenchang, 43–39 Ma) of tectonic reactivation. The fault displacement-length profile further indicates clear along-strike segmentation of the Enping-17 boundary fault, with variations in fault activity playing a significant role in controlling sag formation and internal structural heterogeneity. The structural evolution of the Enping-17 Sag reflects the interplay between pre-existing fault reactivation and regional tectonics along the northern South China Sea margin. Driven by Pacific Plate subduction and India–Eurasia collision, evolving extensional stresses selectively reactivated NE-trending and N–S-trending basement faults during the Early Eocene, facilitating rapid linkage of northern and southern fault segments. Continued clockwise stress-field rotation in the Middle Eocene promoted the development of new ENE-trending faults, while sustained NE-trending and ENE-trending fault activity in the Late Eocene steered the depocenter northward. Ultimately, segmented fault reactivation and progressive linkage, modulated by regional plate interactions, governed the sag's structural complexity and depositional evolution.