Accompanied with rifting and detaching of the north continental margin of the South China Sea, the crust and the lithosphere become thinner away from the continental margin resulting from the tectonic activities, such as tensile deformation, thermal uplift, and cooling subsidence, etc.. In-tegrated with thermal, gravimetric, and isostatic analysis techniques, based on the seismic interpreta-tion of the deep penetration seismic soundings across the northern margin of the South China Sea, we reconstructed the lithospheric thermal structure and derived the variation of the crust boundary in the east and west parts of the seismic profile by using gravity anomaly data. We mainly studied the thermal isostasy problems using the bathymetry of the profiles and calculated the crust thinning effect due to the thermal variety in the rifting process. The results indicate that the thermal isostasy may reach 2.5 km, and the compositional variations in the lithospheric density and thickness may produce a variation of 4.0 km. Therefore, the compositional isostatic correction is very important to recover the relationship between surface heat flow and topography. Moreover, because of the high heat flow characteristic of the continental margin, building the model of lithospheric geotherm in this region is of great importan for studying the Cenozoic tectonic thermal evolution of the north passive continental margin of the South China Sea. Accompanied with rifting and detaching of the north continental margin of the South China Sea, the crust and the lithosphere become thinner away from the continental margin resulting from the tectonic activities, such as tensile deformation, thermal uplift, and cooling subsidence, etc .. In -tegrated with thermal, gravimetric, and isostatic analysis techniques, based on the seismic interpreta-tion of the deep penetration seismic soundings across the northern margin of the South China Sea, we reconstructed the lithospheric thermal structure and derived the variation of the crust boundary in the east and west parts of the seismic profile by using gravity anomaly data. We primarily studied the thermal isostasy problems using the bathymetry of the profiles and calculated the crust thinning effect due to the thermal variety in the rifting process. isostasy may reach 2.5 km, and the compositional variations in the lithospheric density and thickness may produc ea variation of 4.0 km. Therefore, the compositional isostatic correction is very important to recover the relationship between surface heat flow and topography. Moreover, the high heat flow characteristic of the continental margin, building the model of lithospheric geotherm in this region is of great importan for studying the Cenozoic tectonic thermal evolution of the north passive continental margin of the South China Sea.