The Pearl River Mouth Basin (PRMB) is an important area for studying the evolution of continental marginal basins in the northern South China Sea (SCS), but the structural variability and spatiotemporal rifting process remains poorly understood. This study investigates the differential structural features of the eastern, middle and western PRMB, as well as the extensional deformation laws in operation during the rifting stage, according to an integrated analysis of geometric characteristics and kinematic parameters, i.e., horizontal displacement and stretching factors of basin and crust. The PRMB underwent at least three phases of intense extension, which varied in time and space. (1) During the middle Eocene, most sags in the PRMB were intensely stretched and high-angle planar to listric boundary faults controlled the wedge-shaped stratigraphic geometry. (2) During the late Eocene-to-early Oligocene, the stratigraphic geometry of the sags was slightly wedge-shaped and continuously controlled by boundary faults, however, the extensional strength decreased relatively in the Northern depression zone, but increased in the Southern depression zone. (3) During the late Oligocene, the extension was extremely weak in the northeast PRMB, but relatively strong in the southwest PRMB, leading to tabular stratigraphic geometry in the northeast PRMB, but localized slightly wedge-shaped stratigraphic geometry in the southwest. The southwest PRMB still underwent relatively strong extension during the early Miocene. The southwest PRMB that was induced by a small-scale localized mantle convection system constantly rifted during the late Oligocene, controlled by the weak lithosphere, westward (southwestward) diachronous opening and southward jump of the ocean ridge. The applied quantitative parameters and spatiotemporal rifting process may be used as a reference with which to study the segmented continental margin rifts.