Understanding the link between fault activity and movement to petroleum escape is crucial for assessing the petroleum exploration potential in sedimentary basins. As a significant petroliferous basin in China, the Ordos Basin hosts the world-class uncompartmentalized Jingbian natural gas field within the Ordovician marine carbonate reservoirs. However, the role of the unique exhumation history and the Cenozoic faulting in the formation of such large-scale oil-gas fields remain unclear. Our study combines fault-related calcite U-Pb dating with fluid inclusions analysis offers a unique opportunity to trace petroleum leakage along the the carbonate strata brittle fault zones in the SW Ordos Basin. Calcite samples collected from the carbonate fault zone and across the Ordovician carbonate strata in the SW Ordos Basin reveal clear positive Eu anomaly, slight positive Y anomaly, the lack of positive La and Gd anomalies, and the absence of a negative Ce anomaly. The Y/Ho ratios range from 29 to 36, with an average value of 32, indicating calcite formation in a hydrothermal environment during fault activation. U-Pb dating of these fault-related calcites yields ages of 32.8 ± 3.3 Ma and 23.7 ± 7.4 Ma. Raman spectroscopy of fluid inclusions reveals the presence of CH4 gas, coeval with the fault-related calcite. The homogenization temperatures (Th) of aqueous inclusions coeval with CH4 inclusion from two calcite veins range from 140.0 to 172.4 °C (average Th = 157.8 °C, n = 16) and 127.7–154.3 °C (average Th = 142.2 °C, n = 18). Low temperature thermochronology suggest rapid uplift since 40 Ma, potentially linked to fault activity. The Cenozoic erosion rate was 0.06 mm/y during the ∼9 Myr period from 32.8 to 23.7 Ma in the SW Ordos Basin, suggesting that Cenozoic faulting may have created permeable pathways for petroleum escape. This study provides a temporal link between Cenozoic uplift, faulting, and petroleum loss in SW Ordos Basin.