Intracratonic basins tend to subside much longer than the timescale predicted by thermal relaxation of the lithosphere. Many hypotheses have been suggested to explain their longevity, yet few have been tested using quantitative thermo-mechanical numerical models, which capture the dynamic of the lithosphere. Lithospheric-scale geodynamic modelling preserving the tectono-stratigraphic architecture of these basins is challenging because they display only few kilometres of subsidence over 1000 of km during time periods exceeding 250 Myr. Here we present simulations that are designed to examine the relative role of thermal anomaly, tectonics and heterogeneity of the lithosphere on the dynamics of intracratonic basins. Our results demonstrate that initial heterogeneity of accretionary continental lithosphere explains long-term subsidence and the arches-basins architecture of Saharan type intracratonic basins at first order. The simulations show that initially heterogeneous lithospheres inherited from accretion are strong enough to resist local isostatic re-equilibration for very long period of time. Indeed, the lateral density variations store potential gravitational energy that is then slowly dissipated by differential erosion and slow vertical movements. For relatively well-accepted coefficient of erosion of 10−6 m2/s, the subsidence last longer than 250 Myr. Extensional tectonic forcing and thermal anomalies both result in an effective strength drop of the lithosphere, which allows a temporal acceleration of local isostatic re-equilibration. Periodic changes in far field tectonic forcing from extension to compression complicate the tectono-stratigraphic architecture (intra-basin arches, sub-basins) introducing stratigraphic unconformities between different neighbouring basins such as the ones observed in North Africa.