The lack of effective paleogeothermometers restricts the study of the thermal history of carbonate strata. Carbonate clumped isotope thermometry and in-situ U–Pb dating are appropriate for reconstructing the thermal history of carbonate strata. Herein, this study analyzed clumped isotope compositions and U–Pb ages of calcite fabrics, including micrite matrix and veins, from Permian carbonate strata in the eastern Sichuan Basin. U–Pb dating of the micrite matrix was performed to rule out the influence of recrystallization and determine the diagenetic age of the samples. Clumped isotope temperatures of the four micrite matrix samples ranged from 102 °C to 137 °C. The maximum paleotemperature derived from a solid-state reordering model was between 210 °C and 220 °C. From all four samples, three calcite veins yielded crystallization temperatures corresponding to 160 ± 10 °C, 60 ± 10 °C, and 29 ± 4 °C, as determined by clumped isotope and solid-state reordering model analyses. In-situ U–Pb dating provided corresponding crystallization ages of 159 ± 17 Ma, 256.6 ± 5.5 Ma, and 17.86 ± 0.8 Ma. The crystallization ages and temperatures of the three calcite veins align well with the thermal history of the Permian strata, indicating a high degree of accuracy. This study introduces a new strategy for reconstructing the thermal history of carbonate strata. The thermal history can be quantified using the constraints of the crystallization ages and temperatures from different stages of calcite veins or cements. This approach is suitable for determining the maturation progress of the source rock and conducting oil and gas exploration in petroliferous basins.