The thermal evolution of source rocks in the Paleozoic has long been a problem to petroleum exploration in the Bachu uplift, Tarim basin, since the thermal history in the Paleozoic could not be rebuilt objectively due to lack of effective thermal indicators in the Lower Paleozoic successions. The apatite and zircon (U-Th)/He thermochronometry can be used as a new kind of technique to study the thermal history and tectonic uplift of sedimentary basins. Based on the measured apatite and zircon (U-Th)/He ages, apatite fission track data and equivalence vitrinite reflectance (%EVRo), the tectonothermal histories in 5 wells of the Bachu uplift were modeled. The modeling results show that there was relatively high gradient at the Early Paleozoic in the Bachu uplift and it decreased gradually during the entire Paleozoic: 33–35°C/km in the Cambrian-Ordovician, 32–33°C/km in the Silurian-Devonian, 30–32°C/km at the end of Carboniferous and 27.5–31°C/km at the end of Permian. Therefore, the thermal history can be modeled by combining multiple thermal indicators of AFT, (U-Th)/He ages and EVRo data. Especially, this provides a new method to rebuild the thermal history for the Low Paleozoic carbonate successions in the Tarim Basin.