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A series of Cenozoic rifted basins developed in the northern margin of the South China Sea (SCS). Tainan Basin is one of these rifted basins near Taiwan, lying in the outer margin. We have used reflection seismic data in the deepwater areas and boreholes drilled in the shelf of the Tainan Basin to understand the tectonic and sedimentary development in the northern SCS margin near Taiwan. Four key stratal surfaces (i.e., the base of the Pleistocene Series, the base of the Pliocene Series, the 17 Ma maximum flooding surface [MFS], and a breakup unconformity of approximately 30 Ma in age) and seven seismic facies (i.e., continuous-and parallel-layer seismic facies, wavy seismic facies, chaotic seismic facies, U-shaped canyon-cut seismic facies, imbricated-layer seismic facies, high-amplitude reflector package seismic facies, and extrusive volcanism seismic facies) are recognized from seismic data with ages constrained by borehole stratigraphy drilled in the shelf. We have established a model for Cenozoic tectonic and sedimentary development in the rifted northern margin of the SCS near Taiwan. The occurrence of Paleogene fault-bounded grabens/half-grabens topped by a breakup unconformity and draped by postrift sediments indicates that these deepwater rifted basins developed on the continental crust, attesting that a thinned continental crust underlies the deepwater study area, rather than oceanic crust as reported in some literature. Postbreakup extrusive volcanic bodies, of early Miocene age, were buried by thick deepwater sediments. Fairly continuous stratal surfaces of 17 Ma MFS reveal that volcanic activities ceased to be active since middle Miocene. A series of channel cut-and-fills is observed in late Miocene, Pliocene, and Pleistocene strata beneath and to the south of the modern Formosa Canyon. Two distinct fields of deepwater sediment waves developed since middle Pleistocene are found lying to the west of modern deformation front/Manila Trench and to the north and south of the Formosa Canyon, respectively.