The Los Humeros volcanic complex is a geothermal field in Mexico that is now being further investigated as a candidate for the development of a super-hot geothermal system, as it has a temperature of over 350 ∘C. The European Horizon 2020 project GEMex (2016–2020) worked in this context aiming to characterize the geological and geophysical aspects of the area to assess the feasibility of a super-hot geothermal system. We describe the results of time and depth processing and interpretation of legacy 2D reflection seismic lines acquired in 1998 to study the deep structures of the caldera in the Trans-Mexican Volcanic Belt. The study is relevant for the geophysical characterization of the subsurface in this area, where no vertical seismic profiles are available but only two short sonic well logs. The interpretation of selected seismic horizons in the seismic depth profiles was first determined by the local geological model of the curved caldera and then calibrated by the stratigraphy of the boreholes and the matching of the 2D seismic lines crossing points. The processing outcomes are depth-migrated profiles, the corresponding P-wave velocities and the updated geological models. The main results are the representation of the basement and the identification of the structural make-up of the main units with some of the main faults of the collapsed caldera. Our results provide new insights into the subsurface geometry of volcanic collapses and the geothermal field contained within them at the caldera scale.