Characteristics of present-day heat flow and thermal structure of lithosphere in basins are essential constraints to reveal the tectonic-thermal evolution process and to reconstruct thermal history of the basins, which are of great significance for research of basin dynamics and evaluation of petroleum resources. This work is based on 11 newly measured high-quality heat flow values from well-log temperature data in 102 boreholes, oil-test temperature data in over 400 new boreholes, and thermal conductivity data of 187 samples from 15 wells measured by optical scanning in the Junggar basin. Our purpose is to analyze features of heat flow and reveal thermal structure of lithosphere in this basin. The results show current geotemperature gradients between 11.6∼27.6 • C/km, 21.3±3.7• C/km on average; and surface heat flow between 23.4∼56.1 mW/m 2 ; 42.5±7.41 mW/m 2 on average; which imply a cold basin with low geotemperature gradients and low heat flow. These values in the Junggar basin are distributed in largely consistent patterns, primarily controlled by the structural shape of the basement. They are the highest at the uplift in the east, next at the Luliang uplift, relatively low in the Wulungu depression, central depression, and the uplift in the west, and lowest in the range-front depression of the North TianShan. Beneath the Junggar basin, the crustal heat flow is 18.8∼26.0 mW/m 2 , mantle heat flow 16.5∼23.7 mW/m 2 , the ratio of the former to the latter is 0.79∼1.58, indicative of a thermal structure of cold crust and cold mantle. The distribution of mantle heat flow values accords with topography of the Moho interface, which are high below uplifts and low beneath depressions in the basin.