Abstract Our understanding of continent-ocean transition structures and magmatism in the absence of excessive magmatic additions has been guided by the observations and models developed at the magma-poor Iberia-Newfoundland conjugate margins. Recently these models have been challenged in the South China Sea in light of new IODP Expeditions 367-368-368X. We have used an integrated analysis of high quality seismic reflection and gravity anomaly data, calibrated against recent deep sea drilling results, to investigate margin structure and tectono-magmatic interplay during continental breakup and early seafloor spreading between the SE China-NW Palawan conjugate margins. The Eocene-Oligocene South China Sea rifting initiates in a heterogeneous and likely thermally un-equilibrated lithosphere formed by the Mesozoic Yenshanian orogeny. Gravity and joint inversion methods confirm lateral variation of basement densities across the conjugate margins. Lithospheric and basement heterogeneities induced a rifting style characterized by a series of highly thinned rift basins associated with extensional faulting soling out at various crustal levels. Final rifting in late Eocene triggered decompression melting forming mid-ocean ridge type magmatism, which emplaced within thinned continental crust as deep intrusions and shallow extrusive rocks. This initial magmatic activity was concomitant with continued deformation of continental crust by extensional faulting. Integrated analysis of seismic reflection profiles and gravity anomaly data combined with deep-sea boreholes accurately locate the continent-ocean boundary. We show that the initial igneous crust, continentward of oceanic magnetic anomaly C10n, is asymmetric in width and in morphology for the conjugate margins. The wider and faulted newly accreted domain on the SE China side indicates that magmatic accretion is associated with tectonic faulting during the formation of initial oceanic lithosphere. We suggest that deformation was not symmetrically distributed between the conjugate margins during the initiation of seafloor spreading but evolved asymmetrically until the stabilisation of the spreading ocean ridge around C10n. The analysis of the South China Sea breakup reveals a transient interplay between faulting, magmatic budget and extension rates during the formation of the continent-ocean transition and initial emplacement of igneous crust.