This paper presents a new model of the subsurface structure of the eastern Jaca flexural basin of the west-central southern Pyrenees, by means of subsurface structural maps and four new balanced cross-sections. The study is based on the interpretation of a set of publicly available seismic reflection profiles tied to deep exploration well logs, which constitute a unique database in the southern Pyrenees associated to the gas discovery of the Serrablo field. Investigation of the deep basin structure highlights strong mechanical-stratigraphic contrasts between basement, a competent Upper Cretaceous-Eocene carbonate sequence in the deep basin and a weak infill of Eocene to lower Miocene synorogenicclastic deposits. These contrasts promote the occurrence of various décollement levels and a decoupled style of deformation between intervals of different competence. A contour map for the top of basement reveals a complex structure with lateral variations of the number of thrusts and the displacement on these and local transverse elements.Between the Gavarnie thrust at the southern edge of the Axial Zone and the Guarga thrust at the leading edge of the basement thrust system, three main other basement thrusts are defined below the north-eastern Jaca Basin, from South to North the Fiscal, Yésero and Broto thrusts. In the Meso-Cenozoic sedimentary cover, two low-angle thrusts are mappedin the subsurface across the Upper Cretaceous-Eocene carbonates: i) the deep Oturia thrust, connected upsection to the emerging Oturia thrust known at the surface, and ii) the deep Jaca thrust, drilled by the Serrablo wells, and connected to the emerging Jaca thrust and Yebra de Basa anticline through a zone of disharmonic deformation. The deducedsubsurface geometrical relationships are consistent with the connection of the Gavarnie and Broto basement thrusts to the Priabonian-Rupelian Oturia and Jaca thrusts while the younger Yésero, Fiscal and Guarga basement thrusts emerge at the South Pyrenean thrust front of the Sierras Exteriores, active until the early Miocene. This study highlights the complex structural pattern that characterizes the deep structure of the South Pyrenean basin and the role of disharmonic deformation that challenges the resolution of the deeper thrust system without the help of seismic profiles.