The thermal history of boreholes in the western Sichuan depression was reconstructed using paleotemperature indicators, such as vitrinite reflectance (Ro), apatite fission track (AFT) and the illite crystallinity index (IC index). The maximum paleo-temperatures reconstructed based on different indicators were compared. The results showed that the western Sichuan depression has experienced a continuous process of denudation and cooling since the late Cretaceous (K3), resulting in a geothermal gradient reduction from ∼26 • C·km −1 to ∼22 • C·km −1 and the removal of 1.3 to 1.9 km of sediment. The surface area has undergone continuous uplift and denudation from ∼80 Ma to 40 Ma, followed by a thermal quiet period until 2.5 Ma. Since ∼2.5 Ma, the geothermal gradient has risen by ∼5 • C·km −1 . In addition, there was high consistency among the paleotemperatures that were reconstructed based on different indicators. Relative to Ro and AFT, the illite crystallinity index is still controversial; more research is necessary before it can be used as a maturity and geothermal indicator for sedimentary rock.