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The reconstruction of thermal history is an important component of basin evolution and hydrocarbon exploration. Based on vitrinite reflectance data, we integrate the paleo-temperature gradient and paleo-heat flow methods to reconstruct the thermal history of Junggar Basin. Compared with present thermal state, the Junggar Basin experienced much a higher heat flow of ca. 80–120 mW/m2 during the Carboniferous. This feature can be attributed to large-scale volcanic events and related thermal effects. The hydrocarbon maturation history of Carboniferous source rocks indicates that the temperature rapidly reached the threshold of hydrocarbon generation during the Late Carboniferous and has never achieved such a high level since then. This characteristic resulted in the early maturation of hydrocarbons in Carboniferous source rocks. Meanwhile, the results reveal that hydrocarbon maturities are different among various tectonic units in Junggar Basin. The kerogen either rapidly broke through the dry gas period so that cracking of gas occurred or remained in the oil maturation window forming oil reservoirs, which depended on the tectonic background and depositional environment. In this study, we present the thermal and hydrocarbon maturation history since the Carboniferous, which has important implications for further hydrocarbon exploration in Junggar Basin.