In the present study the integration between interpreted seismic reflection profiles, available seismic refraction data, 2D gravity modelling, 2D structural restoration and sandbox analogue modelling are used to depict the crustal-scale architecture and elucidate heat flow issues in the ultra-deep water Lower Congo Basin in order to provide a constrained input to the subsequently performed thermo-tectonic and petroleum system modelling of the investigated region. The integrated analysis provides a state-of-the-art of the large-scale structural and basin evolution of the ultra-deep water Lower Congo Basin. Locally hyper-extended and denser continental crystalline crust is revealed in the area of study. Structural restoration indicates anomalously extensive subsidence at a short time-interval (112-98 Ma) just after breakup. Considerable stretching β-factors are revealed within the ultra-deep water region at two modelled transects. Processes that governed the pre-breakup extension have been constrained through analogue modeling. Based on the above multi-fold analysis potential geothermal-gradient scenarios have been considered in petroleum system modelling that shown important effect on the generation history of a pre-salt source rock potentially present in the deep-water.