Based on the geothermal and gravitation methods, this paperinvestigated the rheological and thermal structure of the lithosphere under the northern margin of South China Sea. The result shows that the temperature of the upper crust is 150-300℃ lower than that of the lower crust, and the viscous coefficient of the upper crust is 2-3 orders of magnitude larger than that of the lower crust. It reveals that the upper crust is characterized by brittle deformation while the lower crust by ductile deformation. A channel of lower-viscosity should be formed between the upper and lower crust when the lithosphere is scattered and spreads out toward ocean from northwest to southeast along the northern margin of South China Sea. And, a brittle deformation takes place in the upper part of the lithosphere while a ductile deformation takes place in the lower part of the lithosphere due to different viscous coefficients and temperature. The layered deformation leads the faulted blocks to rotate along the faulting and the marginal grabens to appear in the northern margin of South China Sea in Cenozoic tectonic expansion.