Following the Mw4.9 Le Teil surface-rupturing earthquake that occurred on the Northeastern Cévennes Fault System (NCFS) in France on 11 November 2019, many studies have quantified the earthquake and associated surface deformation (slip distribution and kinematics) to analyze previous events, understand the local structures of the NCFS in 3D, and evaluate the rheology of sedimentary layers within the hypocenter area. However, the geometry of the NCFS at the scale of the Southeast French Basin is poorly constrained and it remains difficult to locate its trace beneath the Quaternary sediments of the Rhône river valley. To address this issue, Électricité de France (EDF) carried out a deep reflection seismic survey along the NCFS, which we interpreted using surface data, well data, and previous seismic data. The resulting 3D model allows us to reconstruct a polyphase geological history during the past 270 Ma, which we divide into three major tectonic phases. We show that all structures in the basin were initiated as normal faults during the Lias and the Early Cretaceous. These structures became more complex during the Late Cretaceous in a transfer fault regime before reactivation as normal faults during the Oligocene extension. The NCFS is directly related to the morphology and structures of the pre-Triassic basement top. We are also able to update knowledge on the geology of the Vivaro-Cévenol area and the structures that have affecting the Southeast Basin since the Mesozoic. In the context of the unprecedented Le Teil earthquake, our new structural model provides further impetus for continuing paleoseismological work that better constrains the seismic hazard in this region, which has been considered a moderately active seismic area until now.