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Terrestrial heat flow plays a vital role in determining the present thermal regimes of sedimentary basins, offering a robust foundation for understanding hydrocarbon maturation processes and the geothermal resource potential. The Junggar basin is one of the largest and most petroliferous superimposed petroleum basins in China. However, research on heat flow is scarce. In this study, 94 new high-quality heat flow values are derived from through borehole temperature analysis and thermal conductivity measurements of rocks. The results indicate that (1) the geothermal gradient in the basin varies from 11.4 to 28.3 °C km−1, with a mean value of 20.9 ± 3.4 °C km−1, and the heat flow varies from 23.4 to 64.5 mW m−2, with a mean value of 45.1 ± 8.4 mW m−2. The overall low geothermal gradient and heat flow are attributed to the continuous cooling during the Meso-Cenozoic. (2) At basin scale, the high heat flow values are primarily concentrated in areas characterized by basement uplift, whereas the low heat flow values are mainly located in the depressions. This suggests that thermal refraction is the primary factor influencing the heat flow variations. (3) Although large-scale development and utilization of geothermal resources face challenges, certain local areas in the basin show promise for geothermal resource utilization. [ABSTRACT FROM AUTHOR]