Abstract: Lithospheric thermal structure is an integrated reflection of heat producing elements, deep thermal state and tectonic-thermal activities, and it also has a significant impact on the evolution of the lithosphere. Based on the correlativity between temperature and seismic wave velocity of deep rocks, we derived the uppermost mantle temperature distributions and thermal lithosphere thickness beneath the Junggar basin and its surroundings at the depths ranging from 75 to 250 km by the seismic tomography imaging model S2.9EA in this study. Utilizing the inverted temperature distribution at 75 km depth as the bottom boundary constraint and the surface temperature as the top boundary constraint, we calculated the crustal temperature structure and surface heat flow variations according to the one-dimensional steady heat conduction equation. A good agreement is found between the surface heat flow variations by the model prediction and the field measurements, which shows the reliability of the method and the calculated results in this study. The results show that lithospheric thermal structure in Junggar basin and its surroundings presents obvious lateral and vertical inhomogeneity, and the thermal structure distribution in shallow layer is consistent with the basin-mountain tectonic features and it has the trait of interchange with the temperature distribution below 150 km depth. Based on the spatial distribution characteristics of high and low temperature abnormal bodies in the upper mantle of study area, the thermal structure features of basins, contact relationships between basins and mountains, lithospheric delamination of Tianshan orogenic belt, tectonic thermal evolution process of basins and mountains, and the remote influence of India-Tibetan plateau collision on the lithospheric upper mantle thermal structure are synthetically analyzed, respectively, which further provide useful reference and information for the geotectonic and deep dynamic analysis of the study area.