Post-rift volcanisms and fault activities are significant for understanding the tectonic-sedimentary evolution of rifted continental margins and associated hydrocarbon entrapments. In this study, a series of post-rift fault-associated volcanic activities have been found in the northern continental margin of the South China Sea (SCS). However, their episodes and relationships with the progressive continental breakup are still doubtful. Here, new 2D/3D seismic, borehole, dating, and biostratigraphic data are used to investigate the characteristics of the post-rift volcanism and fault activities in the Baiyun Sag (BYS), Pearl River Mouth Basin. The newly-found fault-associated volcanic complexes include thirteen submarine volcanic mounds and associated lava flows, together with igneous sills that are mainly composed of basalts and tuffs. Seismic stratigraphic analysis combined with KAr dating from cores confirms that post-rift volcanism in the BYS climaxed along with the breakup of the SCS mainly in three episodes: (1) the first episode near Oligocene/Miocene boundary (23.3 Ma); (2) the second at the middle Early Miocene (17.6 Ma); and (3) the new-found third episode at the late Early Miocene (17.1 Ma). Also, fifty-three syn-sedimentary faults are interpreted, which are characterized by a WNW trending normal fault group separated by an ENE trending transcurrent fault group. And there is evidence that these fifty-three faults were long-lived from ca. 32–17.1 Ma and served as important conduits for the upward migration of the magma. The three episodes of volcanism and tectonic fault activities are related to the progressive continental breakup in the northern SCS margin, and they represent the tectonic signature of the early stage of the post-rift subsidence after the lithospheric breakup which extends to the top of a hypothetical breakup sequence (32–17.1 Ma) in the BYS. Furthermore, this study proves that the diachronous continental breakup in the SCS margin can result in corresponding changes in depositional architectures, along with a breakup sequence characterized by the deposition of a ‘sandstone‑carbonate-shale’ regressive-transgressive cycle. The sedimentological changes and associated tectonic features recorded in the Baiyun Sag suggest an exceptionally active tectonic setting in the time of the formation of the breakup sequence (Early Oligocene-Early Miocene) along the northern SCS margin.