To investigate the thinning of the whole crust, and the contribution of the upper versus lower crust to the stretching since Cenozoic, we calculated the stretching factor of the northern margin of South China Sea with data such as whole crustal thickness, depth of Cenozoic sedimentary basement and the horizontal displacement of faults. An isometric line drawing on whole crustal stretching factor is then obtained. Along the seismic Line 1530 in Baiyun sag, we also calculated the stretching factors of the upper and lower crust. The results suggest that the whole crustal thickness decreases seaward while the whole crustal stretching factor increases from shelf to slope. The Moho upwells highest beneath where the crust is thinned most. The value of the whole crustal stretching factor ranges from 1.5 to 6. Two areas were thinned intensely: the center of Yinggehai Basin, and the Baiyun sag in the Pearl River Mouth Basin. The calculation of the upper and lower crustal stretching factors from DSP1530 in Baiyun sag shows that the original crust of Baiyun sag should be thinned before deformation. Its pre-Cenozoic evolution as well as tectonic position during Cenozoic might be responsible for that. To investigate the thinning of the whole crust, and the contribution of the upper versus lower crust to the stretching since Cenozoic, we calculated the stretching factor of the northern margin of South China Sea with data such as whole crustal thickness, depth of Cenozoic sedimentary basement and the horizontal displacement of faults. An isometric line drawing on the whole crustal stretching factor is then obtained. The results suggest that the whole crustal thickness The seaward while the whole crustal stretching factor increases from shelf to slope. The Moho upwells highest beneath where the crust is thinned most. The value of the whole crustal stretching factor ranges from 1.5 to 6. Two areas were thinned intensely: the center of Yinggehai Basin, and the Baiyun sag in the Pearl River Mouth Basin. The calculation of the upper and lower crustal stretching factors from DSP1530 ​​in Baiyun sag shows that the original crust of Baiyun sag should be thinned before deformation. Its pre-Cenozoic evolution as well as tectonic position during Cenozoic might be responsible for that.