Faults and fractures are central for characterizing the permeability distribution in carbonate reservoirs since they act as pathways for diagenetic fluids that often favor intense rock dissolution and permeability. Usually, high permeability zones and fractures are not easily recognized in seismic data due to limited resolution and they are often associated with higher concentrations of hydrocarbons or even significant fluid losses during drilling, thus creating a challenge for hydrocarbon exploration. In the Santos Basin, southeast Brazil, the pre-salt carbonate reservoirs from the Barra Velha Formation (BVE) are the main hydrocarbon producers in Brazilian Atlantic margin and well-known for being extremely heterogeneous, exhibiting complex dual-porosity systems. In this study, we built a conceptual model of these fracture zones and non-matrix porosity formation that helped narrowing the understanding of these complex systems. The characterization of faults and fractures was carried out using seismic, well-logs, and borehole image data to understand the influence of these structures in the porosity formation along the Barra Velha Formation. In the study area, three fault sets were defined (F1, F2, and F3) from seismic data. F1 represents to the larger faults, while the F3 fault set represents the smaller faults related to the reactivation of F1; both sets being oriented NE-SW. The F2 fault set is associated with the rift formation and is oriented to NNE-SSW. These three fault sets compartmentalized the studied area into different domains, each exhibiting distinct fracture sets. The natural open fractures were formed during the reactivation of rift faults and are oriented mainly NW, NNE-NNW, NE, and ENE and were identified across the entire study area, but with different intensity values. The fracture intensity closely relates to the distance from major faults where the wells with the highest fracture intensity occurs located 150–590 m from the larger F1 fault set. Scan-lines were conducted throughout the area to determine the fault width, and an average value of 1.2 km was established. Seven non-matrix porosity classes were characterized and classified into stratigraphically concordant and discordant non-matrix pore types at well scale through borehole image interpretation. The Barra Velha Formation exhibit higher occurrence of stratigraphically discordant non-matrix porosity related to fractured zones while stratigraphically concordant non-matrix porosity is mainly controlled by the paleotopography of the study area. Overall, non-matrix porosity formation tends to follow an orientation that suggests a preferential dissolution flow towards NE and ENE directions. Intervals with higher silica content shows a positive correlation with both fracture intensity and stratigraphically discordant non-matrix porosities. This work provides a conceptual model about the fractures and non-matrix porosity distribution in pre-salt carbonate rocks that can help address some of associated structural and stratigraphic uncertainties during field appraisal and development.