Assessing the thermal evolution of sedimentary basins is critical for understanding the origin of natural resources (including ores, geothermal fluids, or hydrocarbons) and for deciphering larger-scale tectonic and geodynamic evolutions. Modern reconstructions of past subsurface temperatures mostly rely on thermochronometers that are not applicable to carbonate rocks [e.g., fission-track and (U-Th)/He analyses]. Here, by coupling carbonate clumped isotope (∆47) thermometry and laser ablation U-Pb geochronology on a complete paragenetic sequence, we demonstrate the applicability of an emerging thermochronometer for carbonate bearing-rocks. Paired ∆47 and U-Pb data were obtained for calcite and dolomite phases precipitated in a Middle Jurassic carbonate hydrocarbon reservoir of the Paris Basin depocenter (France). The absolute thermochronological data allow the precise reconstruction of the thermal history of these rocks: from shallow burial temperatures (∼40 °C), occurring in the Late Jurassic, toward a progressive burial and heating stage (up to 87 °C) during the Cretaceous, followed by a cooling stage (down to 69 °C) during the Tertiary uplift of the basin. The inferred time-temperature path based on Δ47/(U-Pb) data is mostly consistent with the thermal scenario independently deduced from organic maturity indicators from the underlying Lower Jurassic shales. The Δ47/(U-Pb) thermochronological data also highlight a thermal anomaly during Aptian–Albian time that requires revisiting the accepted timing for hydrocarbon migration in the Middle Jurassic reservoir carbonates.