This paper takes the South Yellow Sea as an example to show a new method for comprehensive geological-geophysical research such as residual basin and tectonolayering using airborne gravity and magnetic data in China. Based on airborne gravity and magnetic data, by measuring and analyzing stratigraphic density and susceptibility, the depths to the pre-Sinian magnetic basement top, the pre-Jurassic top and the Cenozoic bottom, are obtained by forward and inverse methods constrained by seismic and drilling data; and furthermore, the residual thicknesses of the Sinian–Triassic, the Jurassic–Cretaceous and the Cenozoic are calculated. Based on airborne gravity and magnetic anomalies, the faults in the pre-Sinian magnetic basement, the Jurassic-Cretaceous and the Cenozoic are respectively interpreted by the qualitative and quantitative methods. On the basis of the above study, and combining regional important tectonic events, four tectonolayers are divided in the vertical succession in South Yellow Sea, namely the pre-Sinian magnetic basement, the Sinian-Triassic, the Jurassic-Cretaceous and the Cenozoic. The result shows that there are thick Cenozoic and Jurassic-Cretaceous strata and thin residual Sinian-Triassic strata in the Suzhong-Huangnan depression area, but there are thin or only sporadic Mesozoic-Cenozoic terrestrial strata and thick Sinian-Triassic marine strata reserved in Subei-Huangzhong uplift area and Sunan-Wunansha uplift area. The four tectonolayers are very different in structures as well as distributions in plane.