Although the Helvetic nappes of the Western Alps have been widely studied, their style, amount, and timing of deformation during the Alpine orogeny remain a subject of controversy. The discussion partly arises from various interpretations of the external crystalline massifs geometry and of the cover/basement relationships. Here, we apply structural analysis based on new field data, microtectonics, and 3D geological modeling on the Aiguilles Rouges and Mont-Blanc massifs, to better quantify their tectonic evolution and their relationship with the nappe stacking. Our results show large thrusting of the Helvetic Mesozoic sedimentary cover above the Aiguilles Rouges basement towards the WNW. The basal contact of the Helvetic nappes, which we call the Helvetic Basal thrust (HBT), often corresponds to a décollement level localized above the Triassic unconformity, but that locally also affects the basement. We suggest that most of the subalpine ranges are klippes above the HBT, and estimate the shortening of the thrust from previously published cross-sections to be between 13 and 32 km. According to published ages, we argue that the HBT was active in the Oligo-Miocene, between ∼30 and ∼14 Ma. After ∼14 Ma and until ~6 Ma, the HBT is offset by late steep out-of-sequence faults, including back-thrusts and the Mont-Blanc shear zone that was previously a ramp of the HBT. The transition of the major thrust system from the HBT rooting above (east) of the Mont-Blanc to the Alpine sole thrust rooting below (west) of the Aiguilles Rouges occurred between 18 and 14 Ma.