We present a regional, crustal-scale, 3D structural model of the Norwegian continental margin integrating sedimentary and crustal layers from the continental and the oceanic domain. The model includes six sedimentary units, underlain on the continental side by a thinned crystalline crust and a lower-crustal high-velocity body. In the oceanic domain, three crustal layers (2AB, 3A and 3B), thickened at the continent–ocean transition (COT), are modelled below the post-breakup deposits. Two major rift phases with different rift axes (Late Jurassic–Early Cretaceous and Late Cretaceous–Early Tertiary) have caused post-Jurassic subsidence and post-depositional deformation of the pre-Cretaceous units. The modelled COT suggests that the pre-breakup rifting event was related to differential stretching focused at the outer margin and that breakup took place in a ‘base-up’ magmatic process as a continuation of underplating. For the earlier rift event, stretching was distributed over the entire margin and led to accumulation of up to 12 km of Cretaceous deposits. The large sediment thickness of the Cretaceous units requires deep-water conditions and abundant sediment supply and thus coeval offshore subsidence and onshore uplift. All layers indicate a sinistral offset along the Jan Mayen Fracture Zone and its continentward continuation.