The Bongor Basin is an important petroliferous basin in the Western and Central African rift system. The basin's evolution history is featured with a strong tectonic inversion during the Late Cretaceous, which resulted in its unique basin structure and hydrocarbon accumulation pattern. However, due to the complex process of repeated cooling and heating, single sample bedrock thermochronology can hardly provide accurate constraints to its thermal evolution history. In this paper, nine granitic core samples from the crystalline basement in five wells on the northern slope of the Bongor Basin were analyzed using multiple thermochronological methods (apatite U-Th/He, apatite fission tracks and length distribution, apatite U-Pb dating) as well as vertical profiles to obtain a more accurate thermal history. The results show that the samples from all five wells underwent four stages of thermal history: from ∼600 Ma to 135 Ma, the samples cooled continuously from 600 °C to near-surface temperatures; from ∼135 Ma to 100 Ma, the samples were heated rapidly; from 100 Ma to 60–80 Ma, the samples cooled rapidly; and after that, the samples experienced slow differential heating and cooling. The thermal history results show that the key time for the strong inversion of the Bongor Basin was between 80 and 90 Ma when the basin was uplifted and exhumed as a whole, while samples in different fault blocks underwent differential uplift and subsidence since the Paleogene.