The uncertainty surrounding the thermal regimes of the ultra-deep strata in the Tarim and Sichuan basins, China, is unfavorable for further hydrocarbon exploration. This study summarizes and contrasts the present-day and paleo heat flow, geothermal gradient and deep formation temperatures of the Tarim and Sichuan basins. The average heat flow of the Tarim and Sichuan basins are 42.5 ± 7.6 mW/m2 and 53.8 ± 7.6 mW/m2, respectively, reflecting the characteristics of ‘cold’ and ‘warm’ basins. The geothermal gradient with unified depths of 0–5,000 m, 0–6,000 m and 0–7,000 m in the Tarim Basin are 21.6 ± 2.9 °C/km, 20.5 ± 2.8 °C/km and 19.6 ± 2.8 °C/km, respectively, while the geothermal gradient with unified depths of 0–5,000 m, 0–6,000m and 0–7,000 m in the Sichuan Basin are 21.9 ± 2.3 °C/km, 22.1 ± 2.5 °C/km and 23.3 ± 2.4 °C/km, respectively. The differential change of the geothermal gradient between the Tarim and Sichuan basins with depth probably results from the rock thermal conductivity and heat production rate. The formation temperatures at depths of 6,000 m, 7,000 m, 8,000 m, 9,000 m and 10,000 m in the Tarim Basin are 80°C–190°C, 90°C–220°C, 100°C–230°C, 110°C–240°C and 120°C–250°C, respectively, while the formation temperatures at depths of 6,000 m, 7,000 m, 8,000 m and 9,000 m in the Sichuan Basin are 120°C–200°C, 140°C–210°C, 160°C–260°C and 180°C–280°C, respectively. The horizontal distribution pattern of the ultra-deep formation temperatures in the Tarim and Sichuan basins is mainly affected by the basement relief, fault activity and hydrothermal upwelling. The thermal modeling revealed that the paleo-heat flow in the interior of the Tarim Basin decreased since the early Cambrian with an early Permian abrupt peak, while that in the Sichuan Basin experienced three stages of steady state from Cambrian to early Permian, rapidly rising at the end of the early Permian and declining since the late Permian. The thermal regime of the Sichuan Basin was always higher than that of the Tarim Basin, which results in differential oil and gas generation and conservation in the ultra-deep ancient strata. This study not only promotes theoretical development in the exploration of ultra-deep geothermal fields, but also plays an important role in determining the maturation phase of the ultra-deep source rocks and the occurrence state of hydrocarbons in the Tarim and Sichuan basins.