In this paper, a velocity model of the Southern Depression of the Tainan Basin is obtained along with its migrated image from an iterative pre-stack depth migration approach. The Cenozoic strata are uniformly layered with velocities varying from ~1.8 to ~3.6 km s-1. However, the general velocity is slightly lower in the NW segment than the SE. Both fractures and burial depth might be the controls of their seismic velocities. There is an unconformable contact between the Cenozoic and underlying Mesozoic strata with an abrupt velocity jump from ~3.2 to ~4.3 km s-1. The Mesozoic strata are recognized with acoustically distinct reflection patterns (chaotic, deformed and discontinuous) and complex internal structures (uplift, folds and faults). Their interval velocities range from ~4.3 to ~4.7 km s-1 within a depth from ~3.5 down to ~12.5 km, and the maximum depositional thickness reaches up to 6.5 km. Multiple tectonic events such as collision, subsidence and uplift might be responsible for the complexity of the Mesozoic strata.