Heat flow is an objective reflection of the dynamic mechanisms and tectonic evolution process in sedimentary basins. Basins, which formed in different geodynamic setting at different time, show huge difference in terrestrial heat flow. Therefore, the research on the tectonothermal evolution of the basin can not only reveal the geothermal characteristics in different evolution stages, but also effectively constrain dynamic mechanism and tectonic attributes of the basin in the specific geological history. With aiming at features of the deeplyburied, multiplestage and complicated thermal history of the Junggar basin, combined with the present study of geothermal field of basins, this study reconstructed the thermal history of the basin since Permian, using paleothermometers such as vitrinite reflectance and fission track, paleogeothermal gradient and paleoheat flow methods, and further discussed the structural property of the basin during the EarlyMiddle Permian. The study shows that the Junggar basin presented the continuous evolution feature of heat flow since Early Permian. During the Permian, the Junggar basin experienced much higher heat flow of around 75~85 mW/m2, even higher than 100 mW/m2 in a few boreholes located in the central depression and southern depression. During the Mesozoic to Cenozoic, the heat flow in the basin maintained and gradually decreased until to the present of 425 mW/m2. During the EarlyMiddle Permian, the highest heat flow area in the basin was distributed mainly in central depression and southern depression. High heat flow resulting from the intensive lithosphere stretching and thinning suggests that the Junggar basin was a rifting basin during the EarlyMiddle Permian, which is supported by many geological, geophysical and geochemical data. The realization is the important basis for understanding the collisional orogenesis and intracontinental basinmountain system transformation during the Late Paleozoic, but also of great significance in deepening the Carboniferous and Permian deep oilgas exploration in the Junggar basin.