Complex structural styles of foreland basins and limited temperature data hinder our understanding of the characteristics and genesis of geothermal systems in these basins. Characteristics and genesis of the present thermal regime in the southern Junggar Foreland Basin are discussed and a conceptual model of the geothermal system is established based on steady-state temperatures, well-testing temperatures, thermal conductivities, radiogenic heat production, and thermal structures. Thermal conductivities of mudstone, sandstone, and volcanic rocks exhibit normal distribution patterns, with their average thermal conductivities in a consistent order. Heat production varies according to lithologic assemblages and uranium anomalies, being higher in mudstones and tuffs and lower in sandstones and coal measures. The geothermal characteristics are predominantly controlled by tectonic patterns, including geodynamic process and current basement structure. Surface heat flow is decreased from the first structural belts in the south to the third structural belts in the north and is converged from sub-depressions to sub-uplifts or anticlines, whose distribution matches well with positions of three structural belts. The generally low geothermal characteristics are attributed to thick thermal lithosphere and crust, as well as the thermal structure of “cold crust and cold mantle”. Groundwater and fault activities also influence heat flow. Additionally, uranium anomalies at the Cretaceous and Jurassic strata in the first structural belts enhance radiogenic heat production and result in continuously-distributed high heat flow. The heat generated by uranium anomalies helps explain the heat flow distribution in the first structural belts, which cannot be fully accounted for by tectonic-related thermal genesis alone.