The South China Sea (SCS) is one of the largest marginal sea in southeast Asia. The northern continental margin of the SCS has been considered an intermediate between the magma-poor and magma-rich end members. Baiyun sag is located in the deep water area where the northern continental crust had been hyper-thinned to < 12km. The syn-rifting deposition in the Baiyun sag shows distinct features to a classic rift basin at the shallow water area. Based on the high-resolution 3D seismic data interpretation and drilling logging analysis, we interpret a structural sequence corresponding to the hyper-thinning process before the final breakup of the continent. This sequence is bounded by a classic breakup unconformity and a regional transgression surface in the syn-rift strata of the Baiyun Sag; within the sequence, a set of foreset reflectors suggesting a prograding shelf-margin delta. Analog to the Iberia margin of North Atlantic, we use the definitions of Lithospheric Breakup Surface (LBS) and Breakup sequence (BS) and determine the distributions of the LBS and BS in the Baiyun sag. Based on the logging results, we apply subsidence back stripping to recover the palaeogeomorphology background with the development of BS. Finally, based on isostasy, we restore the basin structure using the balanced section technique and analyze the controlling factor of coarse-grained deposition distribution. Our results refine the deposition process related to the hyper-extension and the final breakup of the continental margin.