The depth-dependence of crustal extension factor is considered as an important indicator to understand lithosphere evolution. We used the crustal layering model to estimate extension factors both of upper crust and whole crust along the deep seismic profiles carried out in the Qiongdongnan basin areas, northern continental margin, South China Sea. The results demonstrate the obvious depth-dependence of extension factor within crust (the factor ranges within 1.0~2.0 for the upper crust and 1.2~2.5 for the whole crust); the spatially lateral heterogeneity of crustal extension factors and anisotropy (the extension factors in NW-SE larger than in NE-SW indicating the dominant extension direction of NW). These results suggest the predominating extension direction in the northern continental margin of South China Sea and different extension processes occurred in the western and eastern portions of the studied area and/or different mechanisms controlling the extension. Integrating the related geological, geophysical and geochemistry dataset, we infer that the depth-dependence of crustal extension factor and probably simultaneous occurrence of mantle exhumation are resulted from large-scale lithosphere extension in South China controlled by low-angle detachment as simple-shear model.