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A better understanding of constraining paleo fluid circulation along fractures in tectonically complex regions is essential from the scientific perspective and in exploiting sustainable geo-energies such as geothermal resources, but it remains a challenge. Jebel Madar in Oman as a salt dome is an ideal case study because of the complexity of its tectonic evolution and diagenetic process history. Here, we investigated the Cretaceous carbonate-encasing rock of salt domes and calcite-infilling fractures, making them an ideal case study for paleo fluid flow. The objectives were to test two different hypotheses: (1) to verify the previous study based on seismic data that the Hawasina Nappe had been priorly emplaced at the study location and was subsequently completely eroded, and (2) that the complex history of paleo-fluid flow existed in the fractures of the salt dome, and that this system was not yet fully constrained by previous studies, and also including accounting for the presence of any kinetic fractionation. To achieve our objectives, we applied carbonate clumped isotopes on different generations of veins as well as on the carbonate cement of the host rock itself to reconstruct paleo temperatures and the isotopic composition of the paleo-fluids. The carbonate clumped isotope temperatures indicate that calcite vein precipitation occurred between 48 and 171 °C. Assuming that our carbonate clumped isotopes data faithfully capture the recrystallization temperature of the limestone, the geothermal gradient during the Campanian can be estimated at 33.5 °C km−1, implying that the Hawasina Nappe must indeed have been present at the location. We also argue that the evolution of fluid flow in the study area comprises two distinct episodes of fluid circulation. The first episode led to the precipitation of high-temperature calcites followed by closed-system recrystallization during the local emplacement of the Hawasina Nappe. The second episode of fluid circulation occurred at lower temperatures with calcite members representing meteoric diagenetic fluids with evidence of the kinetic fractionation of the clumped isotopes signature in our samples. Our result demonstrates that the new paleotemperature data present new constraints of paleo fluid circulation along the fractures in a salt-domed setting and, importantly, confirms for the first time that the Hawasina Nappe was present at the site of Jebel Madar in the Late Cretaceous. • Structural diagenesis of a salt dome revealed by carbonate clumped isotope thermometry: Study case (Jebel Madar, Oman). • New paleotemperature data present a new understanding of paleo fluid circulation along the fractures in a salt-domed setting. • Confirms for the first time that the Hawasina Nappe was present at the site of Jabal Madar, Oman. [ABSTRACT FROM AUTHOR]