The Tainan Basin is one of the set of Cenozoic extensional basins along northern margin of the South China Sea that experienced extension and subsequently thermal subsidence. The Tainan Basin is close to the Taiwan Arc-Trench System and straddles a transition zone between oceanic and continental crust. A new regional multi-channel seismic profile (973-01) across the region of NE South China Sea is introduced in this paper. In seismic stratigraphy and structural geology, a model of Cenozoic tectono-sedimentation of the Tainan Basin is established. The results show that three stages can be suggested in Tainan Basin; In Stage A (Oligocene (?)-Lower Miocene) the stratigraphy shows restricted rifting, indicating crustal extension. Terrestrial sediments mostly filled the faulted sags of the North Depression on the continental shelf~ Structural highs, including the Central Uplift, blocked material transportation to the South Depression in abyssal basin. In Stage B the Tainan Basin (Middle-Upper Miocene) exhibits a broad subsidence resulting from the post-tiffing thermal cooling. The faulted-sags in North Depression had been filled up. Terrestrial materials were transported over the structural highs and deposited directly in the South Depression through submarine gullies or canyons. This sedimentation resulted in a crucial change in the slope to a modern shape. In Stage C (Latesl Miocene-Recent) a phase change from extension to compression took place due to the orogeny caused by the overthrusting of the Luzon volcanic arc. Many inverse structures, such as thrusts, fault bend folds, and a regional unconformity were formed. Forland basin began developing.