Accurate mapping of crustal thickness variations and the boundary relationships between sedimentary cover rocks and the crystalline basement is very important for heat-flow prediction and petroleum system modeling of a basin. Using legacy industry 3D data sets, we investigated the potential of 3D joint inversion of marine controlled-source electromagnetic (CSEM) and magnetotelluric (MT) data incorporating resistivity anisotropy to map these parameters across subbasins in the Dangerous Grounds in the southwestern rifted margin of the South China Sea, where limited previous seismic and potential field basement interpretations are available for comparison. We have reconstructed 3D horizontal and vertical resistivity models from the seabed down to depth for a area. The resistivity-versus-depth profile extracted from our 3D joint inversion models satisfactorily matched the resistivity and lithologic well logs at a wildcat exploration well location chosen for model validation. We found that the maximum resistivity gradients in the computed first derivative of the 3D resistivity volumes predict a depth to basement that matches the acoustic basement. The models predict the presence of 2 to approximately 5 km thick electrically conductive () sedimentary cover atop an electrically resistive () crystalline crust that is underlain by an electrically conductive () upper mantle at depths that vary laterally from approximately 25 to 30 km below sea level in our study area. Our resistivity variation with depth is found to be remarkably consistent with the density distribution at Moho depth from recent independent 3D gravity/gradiometry inversion studies in this region. We suggest that 3D joint inversion of CSEM-MT, seismic, and potential field data is the way forward for understanding the deep structure of such rifted margins.