Different hypotheses have attempted to explain the long-lasting subsidence of the intracratonic basins,characterized by prolonged intervals of low rate subsidence, alternating with episodic accelerations in subsidence rates. Among them, the Congo Basin (CB) occupies a large part of the Congo Craton, derived from the amalgamation of different cratons. Previous studies demonstrated that the CB formed from a rift phase, during the late Mesoproterozoic. This extensional phase could have been the effect of the action of a slow multi-directional extension on a cratonic lithosphere, which has induced the initial subsidence of the CB. We investigated this tectonic scenario with 3D numerical thermomechanical models, using bi-directional N-S/E-W intra-cratonic extension with uniform velocity applied for up to 200 Myr. We assumed that the amalgamation of several cratonic blocks left a rectangular region with warm and more fertile lithosphere in the model centre, having a size of 10 % or 20 % of the total model area. Numerical results show the formation of an almost circular subsided area in the central part of the model, due to the crustal and lithospheric hinning above the asthenosphere upwelling. We also observe series of topographic highs and lows inside the subsided area and significant uplift at the transition zones towards the almost undeformed cratonic parts. At a later stage (>100 Myr), the topographic depression becomes intersected by two nearly orthogonal, elongated rift structures (quadruple junction), which tend to raise their surface topography. These features well represent the first order heterogeneity characterizing the CB basement, considering that its depth has been further modified by tectonic and climatic events. The formed structures are input for static and dynamic forward gravity models and the outputs compared with the present-day gravity field. In this way, the consistency between the modelled and observed main structures of the CB is demonstrated.